My scenario involves a high sci-fi setting, where starships are readily available to civilians with sufficient qualifications and money. Most civilians would not be fueling ships with antimatter though, as it would primarily only be used in warp drives, which only larger capital ships or specialized exploration vessels would have. In this setting, antimatter is relatively abundant, with basically anyone with a ship that needs it being able to acquire it. The problem with antimatter, as you probably know, is its capability of creating massive explosions when it annihilates. Is there any conceivable reason that could prevent antimatter bombs from being commonplace and keep any Joe Schmo with an antimatter fuel cell from instantly obliterating a capital ship while still allowing plasma based projectiles to be viable?
Anti-matter is still not easily store-able but is instead made on-demand inside the ship in some kind of "charge reversal chamber" (possibly with the aid of some kind of 'unobtainium' which would then become the defacto fuel being bought and sold in place of the anti-matter it produces).
since anti-matter cannot be stored the maximum damage your ships can do is simply going to be equal to their reactors power-output rigged up to the best weapon they can find, which might still be lot but isn't necessarily nuclear Armageddon levels.
It's possible that major governments to have specialised/expensive/advanced machinery capable of storing anti-matter if you still want some form of anti-matter weaponry in your setting
Expense of containing it
How do you contain anti-matter in a safe way? I don't know, but someone does in your story.
It may be that containing anti-matter is so energy expensive that the only way to power a long-term anti-matter storage unit is with an anti-matter reactor. In that case, only the people with the money to operate anti-matter reactors in the first place could possibly store enough anti-matter to make a weapon.
Jon's Law: Any interesting space drive is a weapon of mass destruction.
Basically, you're in a setting where the average person who can pay is already in possession of a personal WMD. Adding antimatter simply makes the existing problem that much worse, so no, there really is nothing you can do about it.
There are really two problems you should be thinking about here, but luckily they both have reasonable solutions.
The question you asked: Use of home-made antimatter bombs against military assets.
You're thinking "how do I keep home-made antimatter bombs out of Joe Schmoe's hands, but a military ship isn't really going to be worried about that. Joe Schmoe with a home-made antimatter bomb is equivalent to the modern US Navy facing a pissed off white nationalist with a ton of fertilizer in a fishing boat. Yeah, the bomb will do a lot of damage to destroyer if you actually GET it there, but if they're paying any attention at all, Joe Schmoe and his bomb are going to get detected and destroyed long before they're close enough to be a threat to the ship.
The trickier question you didn't ask: Use of home-made antimatter bombs against CIVILIAN assets.
This is trickier because office buildings and cruise ships and hotels and things don't have point-defense weaponry. Terrorism is a much more serious threat when you've got freely available antimatter, but I think you've got a pretty simple solution: Unless your containment system is 100% perfect, you're always going to be emitting radiation as stray atoms of antimatter annihilate with stray atoms of regular matter. A 99.999999% perfect system is good enough to prevent that from causing any damage anybody cares about, but it will STILL result in your antimatter fuel cells having a detectable radiation signature.
Your solution is just to ensure that antimatter fuel cells are only freely available in places where ships are being refueled, and trying to take one anywhere ELSE is going to be immediately detected and result in a giant pile of authorities descending upon you.
You could make it very difficult to contain in the correct way to weaponize it.
We have this issue with nuclear power (thankfully!). It is much harder to get Uranium to explode with the force of a nuclear bomb than it is to get power from it. You have to enrich it first.
One of the major unknowns with using antimatter is containment. Good containment is tricky. The best we have accomplished has contained antiprotons for 16 minutes. Perhaps the only way to store antimatter for any reasonable period of time stabilizes it so well that even if you dismantle the apparatus, it still takes time for the energy to dissipate. Perhaps the antimatter itself is part of the containment, and the antimatter's properties are sufficient to maintain the containment for a short while.
Perhaps vortex math actually provides some useful results. Rodin coils are popular in that community because they are believed to be ... well... I'll just say there's a lot of people who think you can violate the conservation of energy principle with them. Here's an example of something they can actually do.
One of the neat things that happens in these experiments is that you manage to spin something up to great angular speeds, and even if you remove power, the object continues spinning (due to its angular inertia). However, if anything from vortex math turns out to be correct, we might find that "something else" can start spinning, and that spinning stabilizes the antimatter so that it doesn't immediately annhilate.
(Note: in particle physics, we often refer to things as "spin" simply because they have rotation-like properties. This "spinning" could be a new attribute of matter rather than actual physical spinning like the ball magnet in the video)
If this happened, it could take a minute or two for the spin to decay. A weapon that discharges over a minute or two is much less terrifying than one which discharges over milliseconds.
My scenario involves a high sci-fi setting, where starships are readily available to civilians with sufficient qualifications and money.
So you've established that your world has some kind of certification authority (checking qualifications), a central bank (issuing money), and a military (implied in your reference to civilians). Good: A functioning government goes a long way in keeping people from blowing stuff up. Also: This setup implies your story-line takes place during peaceful times, before or after a major war (see final note at the bottom). You must not be already at war, otherwise all civilian ships capable of large-scale destruction would be immediately seized and re-purposed for military use.
In this setting, antimatter is relatively abundant, with basically anyone with a ship that needs it being able to acquire it.
You need to establish a credible process by which someone who needs it actually acquires it. e.g. They have to file flight plans with the competent government authorities before they can take possession of a pre-loaded antimatter fuel cell. Possession of any other container of antimatter is not permitted and attracts immediate government attention.
Is there any reason that could prevent antimatter bombs from being commonplace and keep any Joe schmo with an antimatter fuel cell from instantly obliterating a capital ship while still allowing plasma based projectiles to be viable?
There's a lot of unrelated concepts mixed up in this question.
Preventing bombs from being common-place: this is a good old government function known as law enforcement. In less stable times, it is also known as counter-terrorism, or if you've just invaded another civilization, it's called counter-insurgency. There are also treaties between governments, if your world is multi-polar (as opposed to a centralized empire). This is accomplished by taking entire regions of space where the antimatter is abundant, the extraction machinery, storage and transport technologies and putting them under government control.
Joe Schmo is under control too. For all his money, he is only given a government-issued antimatter fuel cell. Capacity is limited, cells are only filled and programmed to fulfill approved flight plans.
Capital ships, assuming these are military ships, wouldn't just let a civilian starship sneak up into blast range (further reading: Are nuclear weapons useful in space?).
Plasma based projectiles only require microscopically small quantities of antimatter to be lethal, so yes you can still have that.
You didn't ask, but I'll add: all civilized star systems are equipped with a security perimeter that can detect approaching antimatter, and will swiftly intercept any ship that does not slow down and follow approved flight paths. Your populated planets also need to be defended from kinetic attack, but that's a whole other question. Large-scale storage and refueling facilities are kept on the dark side of the Moon. Starships arriving into the Solar system are required to make an inspection orbit around Jupiter. Bringing anti-matter onto any populated planet's surface is strictly forbidden.
The bigger picture:
Your universe needs a Doomsday Clock, a countdown to Galactic Nuclear War
If your universe is peaceful and possesses abundant weapons-grade anti-matter, then this universe must be in one of two states: either A) pre-war: government doesn't have full control, your universe is on the verge of an epic war to stop the terrorists and protect anti-matter resources (think nuclear war on a galactic scale), or B) post-war: your universe has recently emerged from an epic war, and the victors are masters of anti-matter production, deployment and counter-measures (if they weren't, they would not have won the war).
I wrote this whole answer assuming a 'B' type universe. However, a type 'A' could lead to a more interesting plot.
Yes and No, The simplest way to think about it is how fertiliser is handled modern day, if you have a need for it (Farmer or in your case ship owner) you can get it. If you start to buy more than you need for your purpose they halt your purchasing and send investigators to clear you. So your security is making sure anyone who has enough to be a threat would never use it that way, it's not foolproof but that is the tradeoff between safety and usability.
The smoking gun effect
Hydrogen and antihydrogen collisions are going to have some very energetic emission spectra, some of them in the ultraviolet. Other than stars there are very few sources of high energy emissions at these wavelengths (read almost none). So mass production efforts at equipping important terrestial areas and space lanes with cheaply built optical sensors and mesh networking would yield a detection network that would make it possible to do forensic data analysis to say this explosion originated in this very narrow region of space. Woe betide the poor sap who launched the anti-matter bullet when the cops get finished doing a lot of matrix manipulations on sensor data.
You can make the reasonable assumption here that anyone who is making anti-matter on a large scale either has harnessed enough energy to be further along the kardashev scale than we are. Or they have learned considerably more about physics and materials science. Or both. In any event, this makes it almost certain that they have the necessary raw materials and energy to mass produce a mesh network sensor array for multiple wavelengths at a cost scale far below todays standards.
It is a lot harder to get away with breaking the law when everyone sees you doing it.
Containment is a trade secret and has safeguards
Perhaps only a single company/species knows how to create antimatter containment (or generate anitmatter at the moment of use or teleporting the antimatter to the user's location, for all we know--they are not telling) and they have specialized technology to do so. Said technology has safeguards so that it limits the amount of antimatter that can be output at a time based on the size of the ship it was installed in. Attempts to break into the device to reverse engineer the technology have only led to the timely deaths of those investigating and of course exercising the ruinous penalty clause (probably against the entire planetary system of the flag of the device, making each species very eager to enforce the rules) of the rental agreement.
How does the company get new customers? Perhaps an exploratory advertising branch that puts plaques on the far side of the moon (or whatever is convenient in-system) of potential species with a little radio transmitter good for a few million years with instructions on how to build a FTL beacon that requires a certain level of technology. Of course, for all we know maybe they seed life-bearing world to create their customer base. A high-technology rich species with a long term outlook of millions of years.
You would need to create it somewhere else or you would need to use some other fuel to create it first, which would beg the question why you wouldnt use that fuel directly. The implication of this is that you can readily store it without it detonating within your ship until you need it. If you can store it you can also prevent an anti-matter warhead from detonating on your hull, for example by using a larger version of whatever antimatter manipulation you have to prevent the antimatter touching the insides of your ship on the outside. Alternatives like using antimatter similar to a nuke (have it react with some matter in the warhead) might be easier to stop or detonate prematurely, for example with another antimatter warhead or long-range antimatter manipulation.
As another alternative: large ships are only capable of space drive travel. The assumption is that the drive needs to be big or specialized so only large ships can carry them. But what if only large ships can safely transport antimatter? This means any antimatter weapon would immediately be too small to contain the antimatter safely till it reaches the target. Launching "naked" antimatter would mean any matter fired into it would immediately disperse the antimatter and render it mostly harmless if not detonate too close to the ship firing it.
In order to keep anti-matter from being weaponized there should be multiple prohibitive layers to actually extracting energy from anti-matter. I will outline some examples here.
Anti-Matter Creation is Prohibitively Expensive
It is currently incredibly difficult create anti-matter "on-demand", and certainly not in large quantities. Perhaps, technological advancements have been made such that this substantial improvements have been made, but it is still extremely expensive for anyone outside of heavily funded government entities or extremely well-funded private corporations to do so easily. This likely requires specific purchases or rare elements, that could be regulated or monitored much the same way deadly compounds are monitored today.
Anti-Matter Storage Is Prohibitively Expensive
If you are using anti-matter as an energy source you likely want to store it somehow. Even though the technology exists, even in your world it is still difficult and expensive to safely store sufficiently large anti-matter quantities. Once again, it likely has specific requirements in terms of items to purchase to achieve which could be monitored.
Amount of Anti-Matter Needed for a Weapon Is Prohibitively Large
For use of anti-matter as fuel, maybe you only need a small amount to be sufficient, or a small rate of production. For a large-scale weapon, you might need a large quantity. Even if a person is able to create and store a small amount, it is not enough to make anything more dangerous than conventional explosives, and is more expensive.
Use as Fuel Needs to Not be Too Prohibitive
I just listed off some reasons how to make anti-matter hard to use. But how then can it be so commonly used as starship fuel? Couldn't you just siphon some from your starship's tank?
What I propose is that starships have been able to get around some of the above restrictions by exploiting some of the differences in use-cases between fuel and weapon.
The starships engine is not an anti-matter storage container, and the fuel is not anti-matter. The fuel is instead a rare and expensive element or compound that produces a specific rate of anti-matter particle emission through radioactive decay when combined with a small amount of another specific element or compound (let's call it a catalyst). Otherwise it is inert. The engine then combines the two substances within a specific chamber and immediately harvest the energy. No storage is needed at all for the anti-matter, and the rate of anti-matter production is only suitable for a continuous relatively slow reaction (i.e. like a burning match, the reaction is too slow to cause a runaway reaction).
Now an intrepid terrorist can easily get ahold of the fuel, and the catalyst, but will not be able to store enough of the produced anti-matter to weaponize it. Other methods to create large quantities of anti-matter in a short time are prohibitively expensive, so that is out as an option also.
BONUS: Since the engine gets around the need to store the anti-matter, have the emitted anti-particle be electrically neutral, such as an anti-neutron. Since charged particles like a positron are orders of magnitude easier to capture and store compared to neutral particles, even though there is a continuous source of anti-matter, it is even more difficult to capture and store it.
The question could be answered by starting from a similar question:
Since flammable liquids are common vehicle fuels, what prevents them from being commonly weaponized?
Indeed, the majority of contemporary weapons don't use destructive potential of common fuels, they mostly use them as, well, fuels. Why is that? Probably because common-fuel-based weapons are not very powerful, effective and safe to use (although some are still occasionally used in guerrilla warfare, e.g. Molotov cocktail). Even VBIEDs/SVBIEDs don't use their fuel as a (primary) source of explosion.
Similar situation may arise for antimatter fuel. The fuel-based antimatter bombs could be so terribly impractical that it might be simpler to obtain more conventional weapons. For example, the fuel might be stored in a lot of hard-to-break containers with a relatively low antimatter content.
Add a common belief that antimatter fuel can't melt space station beams and your terrorists and guerrillas will use other means to try to achieve their goals.
I think the best way to prevent antimatter use as a weapon is to simply have it be incorporated into your ship, so that you have to crash your entire ship to actually have it react to anything. During normal operation it'll be locked into a stasis field or whatever is on your ship that prevents it from exploding you.
Now if someone does crash a ship, there's a good chance of an antimatter explosions happening. Perhaps most cities will have anti crash buffers in place that will magnetically control a ships decent, locking it in place if it seems to be crashing? That would at least deal with your landing sites.
Another way that comes to mind is to use quantum teleportation to control antimatter. Have your antimatter entangled with the inside of a vacuum tube with the quantum particle you're using. Then you buy that unit and download the entanglement specs onto your ships computer. Now your ship can only access a single molecule of antimatter at a time whenever you engage the entanglement function. That would at least prevent someone from having a lot of antimatter at once, so long as bein locked into the engine is the only way to prevent it from exploding the ship.
Anything can be Weaponized
The task is to keep it from irresponsible people
Antimatter can be stored as positronium hydride (a hydrogen atom bound to an atom of positronium) to keep from extreme damage when touching anything. Using this compound lowers the risk of catastrophic incidents. Anything can happen when you involve humans in anything.
Since Antimatter in your cas is mainly obtained through a spaceship, a system might have to be put in place that any interactions involving antimatter are computer controlled on a closed system. Internal specialists will have to be searched before entering and exiting the plant, and should work there no more than a week or so. This will keep internal sabotages at bay.
Then there is the case where an attack on an antimatter fueled ship could result in the annihilation of antimatter in extremely catastrophic ways, the same when an antimatter spaceship wrecks. This can be minimized through antimatter fuel cells, but again, anything can happen with humans.
The question you are trying to solve is about minimizing the risk of an antimatter attack, and preventing any antimatter fueled attacks means no use of antimatter whatsoever.
Antimatter as a Catalyst, Not an Energy Storage
You said that antimatter was only used in warp drives. Well, warp drives are weird, let's make them use an exotic ingredient, antimatter, but only as a catalyst of sorts. Perhaps a (smallish) ring of anti-molybdenum is needed to convert neutrons from a nuclear power source into warp energy.
However, the anti-molybdenum slowly decays as the neutrons impact it, so it must be replenished after every voyage. This is an easy task due to the revolutionary Mr. Accelerator™ devices, which can produce small quantities of antimatter (maybe a milligram or so a week).
These devices are expensive, and only governments can afford to have enough to restore anti-molybdenum rings. The antimatter is immediately transported to the ships and installed on the rings. Better yet, it it made in situ.
Additionally, the antimatter is only stable in space in vacuum under a solid 10 meters of lead (or uranium, your choice). Due advances in 3D printing, a 3D printed frame of anti-neodymiun-iron-boron holds the anti-molybdenum ring in place, and is in turn secured by immense (regular matter) neodymium-iron-boron magnets. To remove the rings, you would need to some how break the laws of physics and turn of permanent magnets.
What stops people from using the Mr. Accelerator™ devices to make antimatter warheads? The ridiculously small amount of antimatter it produces per unit of energy. It just isn't economical to build trillion-dollar warheads just for most of them to miss a space ship.
And against civilian targets? Antimatter weapons are by no means small. They are also much too heavy to be much use on planets. It's just easier to use a fission (not even fusion) bomb.
If your society has spaceships and starships and antimatter fueled warp drives, it is probable that it has slower than light ships that can reach relativistic speeds, and faster than light ships that travel at multiples of the speed of light.
Space ships that can travel that fast make terrifying kinetic weapons, regardless of their power sources. The impact of such a ship with another objects is likely to cause an explosion similar to or greater than the explosion of its fuel supply without a collision would be.
So the deadly danger would be the spaceships as well as any antimatter fuel they contain.
Therefore, spaceship trajectories would be highly regulated anywhere near a solar system with inhabited planets. Spaceships that approach the solar systems with threatening orbits, or spaceships within the solar system that suddenly deviate from their approved orbits, would be attacked, vaporized, and/or diverted first and questions asked later - if there are any survivors or intact flight recorders.
In the Star Trek: The Next Generation episode "Haven" (30 November 1987) an unidentified spaceship is approaching the star system of the planet Haven. Valeda Innis, the First Electorine of Haven, calls the starship Enterprise which happens to be in the Haven system:
VALEDA [on viewscreen]: An incoming vessel has bypassed our stargate, violating our law. It has refused any attempt at communication.
PICARD: Are you saying you believe it to be hostile?
VALEDA [on viewscreen]: Failure to communicate is inherently hostile. We have no defensive capabilities here and our treaty with the Federation specifies your obligations in that matter.
The stargate is not described and it is uncertain what percentage of other star systems have stargates.
It is possible that the stargate is the exit point of a some sort of space warp leading to another solar system. The voyage through that space warp bypassing many light years of space could be much shorter and faster than travelling though those light years of space, even with warp drive.
Because of the many, many, many problems and inconsistencies with speed, distance, and time in every Star Trek production starting with TOS, there is a theory that many interstellar voyages in Star Trek involve travelling through one or more of those hypothetical space warps to vastly shorten the journey length and travel time.
So the idea that the stargate in "Haven" could be the exit of some type of space warp used for interstellar travel is very attractive.
Another possible theory is that the stargate in "Haven" is some type of vast space fortress that all spaceships that approach the system have to match velocity with and dock with. The spaceships are inspected for contraband and alien germs and the passengers and crews checked. Then the crews would probably be sent to the destination planet as guests/prisoners in a separate spaceship manned by a Haven crew and another Haven crew would board the ship to take it to Haven.
All Haven citizens allowed to operate spaceships in the Haven system would be psychologically profiled and selected for extreme loyalty to Haven, and their families would be held as hostages. Whenever a spaceship deviated from its assigned course the families would be tortured and images of the torture broadcast to the spaceship until it returned to the assigned course.
Presumably a Federation starship would be exempt from the requirement to stop at the stargate.
Antimatter would also be very strictly controlled. Antimatter would be produced in gigantic space factories far from anything that could be damaged by a gigantic, planet-devastating, explosion. The antimatter that was sold to customers for spaceship or other use would be in containers and legally considered to be "Sealed Evil in A Can".
Because misusing a tiny amount of antimatter is equal to releasing Cthulhu upon an unsuspecting world.
Presumably the containers, and the spaceships and installations that used antimatter, would have complex AI programs to determine whether the antimatter is being used properly and whenever the programs suspected intent to misuse the antimatter they would unleash killer robots to kill first and ask questions later.
Thus the spaceship-using or antimatter-using characters in your story would be constantly worrying and checking that anything that they did with spaceships or antimatter was not only legal but also didn't appear to be even the least bit suspicious, since they would live in constant fear of the horrifying penalties for doing anything that seemed even the least bit suspicious with their spaceships and/or antimatter.
Antimatter Storing Crystal
If antiprotons could be stored in a special crystal, (ordinary protons can absorb/conduct in certain materials, so maybe there might be a way for antiprotons to do so), then it could be tied up this way that makes it tough to access a lot of it all at once.
I'm imagining a crystal with a certain central axis of symmetry. When a small voltage is placed at a right angle to that axis, it breaks the symmetry allowing particle-antiparticle collisions, which somehow produces a current (I'm imagining the antiproton-proton pairs sitting in molecular holes (holes like in the center of a buckyball)).
A larger voltage can produce a larger current, but only up to a point of saturation. So while these crystal store a great deal of energy, there are limits on how much power can be delivered at any particular point in time.
Antimatter Bombs are Useless
An antimatter reactor is a piece of precision hardware the likes of which humanity has never constructed before, Every second of its operation requires constant monitoring and if anything goes wrong there's an ungodly explosion. The people who work with them are serious, careful and procedure-oriented.
The hardware itself is a monolith of technology the size of a small spacecraft on its own.
If you wanted to explode such a reactor then you'd merely have to shut down its containment systems for a moment, but to do that, you'd have to get past every safeguard, security guard and the full defences of an active war-footing capital ship.
Such technology is strictly regulated and prohibitively expensive, the only non-military organisations who operate them are staggeringly wealthy interstellar corporations who operate their own private armies and can readily defend their equipment as well as any military would.
Anti-matter bombs are no different. they are unstable, requiring perfect containment for their entire operational lifespan. They are the last word in Mass Destruction. Their mere existence courts disaster and no government will tolerate anyone having access to them.
But they're also the most unwieldy weapon ever devised. A ball of sophisticated technology the size of a small building, regulated by a crew of a dozen highly educated men and women until the day comes that they set it on a timer and flee the scene.
Such devices are worthless as weapons of war. Too large, too cumbersome and far far too dangerous.
Instead, they're used to wreck moons and as statements of power.
"We can build this, what can you do?"
Econony and Effectivity is the key
Antimatter is expensive (energetically).
As there is not natural source, it must be done, from nothing, but energy. Basically it is the best energy storage you have at the time, but still it gets a lot of energy to move big interstelar ship and make it warp (or fast enought or what) and all that energy have to be stored in the form of antimatter first.
There are not enought free resources at Earth to create enought AM for all ships. But it is not a problem - we simply have big (as in planetary size big) solar convertors in space, which give us nearly unlimited electrical energy for free (well Sun would waste it sending it to interstellar space anyway, so why not use it). (We would need it anyway in this system)
Everybody and his dog have space ship - we need so much energy for it
Again, if nearly anybody (well anybody rich, but still a lot of people) can have spaceship, there is also need for fuel to move it in space - we use the electricity to break asteroids/comets/... to conventional fuel for in-system travel - and burn it in everyones rocket to something, which could be eventually later harvested and reprocessed again, when it get collected in some proto-asteroids on some convenient places (if terms of hundreds years, maybe)
Also the effectivity to get rocket from gravitational well is just poor today - lets use space elevators, with free electricity we can lift anybody to spaceyard and/or back to ground. In-system (personal)spaceships do not land on Earth, but on such elevator equipped spaceyards as well as personal airplanes are using common airports, not roof of house today.
Antimatter react with any normal matter
So it could be created in large enought quantities only in hard vacuum - basically means space, near of big enegetic source - the solar convertors. While it is possible for Joe Doe to have spaceship, it is not possible for him to have all the equipement needed to cr4ate and store large quantities of antimatter and also large enought power source to create and store it (it must be trapped in electromagnetic fields with large intensity and so large power consumption. Also the technology, to be able mass produce antimatter, must be of proper scale, not just some small facility. And its effects are clearly visible in space, as well as the power sources needed to just maintain it - you cannot hide it in garrage.
Antimatter is needed for interstellar travel
So it is sold only on interstellar spaceports deep in space (say around Pluto or something like that) and is not allowed inside Solar system. (Except for good known and protected routes from solar converter to interstellar ports.) Also as it is unstable, it must be protected by powerfull elmag shields all the time (which is possible to destroy (=put momentary down) with large energetical pulse from the converter, where the energy is abudant - so piracy is impossible, if you do not want explode while trying). The container with elmag shields itself is enought of normal matter to make explosion so large, that you just vapore, if you try to travel near its trace (which is strictly forbidden and ship-computers have coded safely avoidance such risky places as well as avoidance of say Sun itself - not that it could not be hacked with a lot of effort, but it could not be done by mistake, nor by normal interface).
Any approach to AM-container trajection is responded in military style as act of planetary agression (evaporate first, ask later) both by Energy company and any goverment/military in shooting range.
If somebody wants interstellar travel, he takes taxi/heli to nearest airport, plane to base of elevator, lift to spaceport, in-system rocket to interstellar port near Pluto and finally board big interstellar ship - be it (his) private, corporate or govermental (as well as the taxi/heli/in-system ship on his way)
Antimatter evaporates slowly anyway
As it is technologically easier to make antimatter in form of hydrogen/oxygen/any evaporable element (or at least it is presented by press and oficial sources), the antimatter still slowly evaporates, which makes continual reaction with its container and is also reused to power it. It also create clearly visible trace of any container with AM, so it can be tracked over whole Solar system. So "smugling" such container to a planet is impossible, without being detected days or weeks before landing and being evaporated in matter of hours after first detection, if communication is not successfull and such container would not fast change trace from Sun and planetary zone.
Which is responce to your question
Ofcourse it could be militarized by goverment or Energy Company, but being trackable and destroyable by EMP pulse much faster, than delivered to planet surface it is not much of risc, if there are two or more independent powers, which does not want have their Earth headerquarters eveporated by antimatter bomb. (And anti EMP-pulse pulse is not possible to use, as if it is not superexactly coordinated to amplitude and frequency with sub-nanosecond precision, it would explode the container by the anti-pulse power)
As stated, there is much larger risc of clasical near-light-speed ram to planet, but it is probabelly countermeasured by some energy weapons all around the space, conventionally powered inside the system, AM powered on interstellar ports and Sun converters (AM/energy for just launching projectile able to push something few miligrades from its trajectory, eventually evaporating by being hit by the fast attacker (which would do it as well), is a lot less, than energy needed to puch whole atmosphere (and magnetic fields around) and still do massive damage on surface.
Humans probabelly would create such defensive system anyway, as there may be interstellar comets, or what, which could endanger Earth, even without terrorist planning it. Also there is a risc of interstellar ship with failure on its return way - so at time of danger probably all avaiable anti-asteroid lasers on all ships in space would also coordinate to add a little energy to push harm from Earth.
Delivery impossible because containment not self-contained.
As you stated, only capital ships with warp drives have anti-matter drives -- and the facilities to contain antimatter.
Because containing the antimatter requires big facilities... as in, a sizeable percentage of capital ships is dedicated to antimatter containment. Nothing smaller can keep antimatter contained (which also rules out producing antimatter in some smaller facility). You need really big capacitors to buffer even the most minute power fluctuations. The radiation shielding alone weighs tons. Compare fusion chamber containment and scale up accordingly.
You just can't get the antimatter anywhere except from one containment facility (unmanned refuel station) to another (capital ship)... and even that is so extremely tricky that it is only done in orbit. (Also, to avoid some madman sabotaging his AM containment to create a huge explosion planetside.)
If you try to take antimatter out of containment to deliver it to a target... boom.
If you try to take the containment chamber out of the context of a capital ship (or a production / refueling facility) to deliver it to a target... boom.
This of course does not rule out using a capital ship, 9-11-style, as delivery vehicle. Then again, we are talking thousands of tons of mass at escape-speed velocities even without taking warp drives into account... at which point it does not really matter if you're delivering an antimatter payload or just pulverise the target with the kinetic energy of the impact.
How do we stop a WMD from being used? Pretty simple really. It's Cold War solutions. Even though we know the right thing to do for everyone to win is to not do the bad thing nobody expected it to really happen. That said there's more you can do if you're willing to add to the premise:
- Everyone has antimatter Harder stand-off in a Cold War-like situation if the civilians have it in their cellphones.
- Storage is extremely hard given how hard antimatter is to contain, might as well make the storage so durable that you'd need antimatter just to crack it open.
- Education grind the thought right out of them. Possibly with some Big Brother monitoring for good measure.
- Suicidal Attempting to use it as a weapon is most likely going to result in their deaths not from backlash but from backsplash. Feed this fear.
- Manipulation Energy produced by a storage unit is only going to generate at a certain rate. Manipulating such a device to increase output should be impossible for someone not extremely well-versed in the science. Perhaps even then they don't have the required tools.
- Regulation Even if everyone has access to a supply of it. It doesn't mean they have it all at once. A depot could resupply everyone's cellphone battery with a charge that's not too terrifying.
In two words Counter Containment.
Anti matter can only be contained by fields not matter. Trying to contain it with matter produces spectacular but useless results.
So we contain it either with a magnetic or electric bottle.
If you possess a device that can disrupt electric or magnetic fields you can cause antimatter explosive devices to detonate prematurely maybe even so prematurely that they destroy the launching vessel. This is not outside of the realms of possibility in a society that can create and store antimatter.
You are indicating that antimatter is only needed by some major star-going vessels. Therefore, security comes from three things working together:
1) Antimatter storage in vessels is built into the keel. Removing an antimatter storage device from a ship basically requires dismantling it and still yields a very big object because the components are dispersed in the frame.
2) Antimatter storage that can actually be moved around is handled akin to how we currently handle atomic bombs--perhaps a step further by providing an armed escort ship whose job is to destroy the transport container if it's misappropriated.
3) The ships that use antimatter are not allowed anywhere near a planet or other such vulnerable location. Your vector comes within 10 million miles of an inhabited world and the authorities shoot first, ask questions later. Lesser vessels that don't use antimatter provide all the transport near population centers.
If you only deal with one electrical sign at a time, anti-matter or real-matter still obey to electromagnetic field and can be deflected, and so, contained, without having to enter in contact with "real" matter. In theory. As we hope to do for high energy plasma in order to produce controlled and sustained fusion. The size of the equipment to produce the required magnetic field is huge, at least for us with fusion, that this is not "possible" (economically) for a particular organisation to produce one, just for a "single" use (as a bomb). Could be used as a weapon (static location or on a huge movable platform) if the equipment used to generate the em field is not destroyed at each use. And some energy has to be available to supply and maintain that equipment while it has to contain the anti-matter. Such equipment won't be profitable to build with the goal to store a single positron. It would hardly be a hand-held weapon.
Neutral anti-matter won't react as well to magnetic fields, that is why one could held separated positrons and anti-protons (so they don't make an overall neutral anti-Hydrogen atom), while not dealing at all with anti-neutrons or other anti neutral particules, since they could not be so easily contained.
As far as creating and storing antimatter goes, there are several links below that may help. There are devices already in use, and in the process of being finalized for use in order to store, transport, and use antimatter. These videos should point one in the right direction for further answers about the subject. As for not using antimatter as a fuel source, this would probably not be plausible, which can also be explained in the Tedx video below. It would simply take too long, cost too much, etc. Which is one reason why space programs have slowed down today. Many other answers have pointed out the issues with using antimatter as a bomb, but this is not to say it wouldn't or can't be done in some circumstances such as previously mentioned civilian targets. As for differentiation between certain drives, it might make 'sense' in a way for some ships to use a warp drive (Alcubierre drive) for interstellar travel, and use something similar to current antimatter drive concepts for high velocity within a solar system. The problem with the antimatter drive is special relativity (specifically time dilation), which means using an antimatter drive to travel great distances is feasible, however don't expect to arrive or come back to the same time period.
Tedx talk about antimatter and a newly invented device: https://www.youtube.com/watch?v=EBebWBjpWIQ&vl=en
Article about CERN transporting anti-matter, also mentions techniques used to store antimatter: https://futurism.com/cern-transport-antimatter/
warp drive: https://en.wikipedia.org/wiki/Alcubierre_drive
Antimatter explossions are too random to be efficient.
Ok, it is very powerful and reactive. But that is precisely what makes it very inefficient.
As soon as the antimatter is exposed to matter, its outer layer desintegrates and pushes the rest of the mass in the antimatter. While the explosion is perfectly simmetrical it is ok and the antimatter does not move much, but... what happens if one of the sides gets in contact with more matter (and thus desintegrates more and pushes more the lump) than the other?
For example, your lump hits a building, or the ground, or even crosses a zone of colder (denser) air, and your bomb gets thrown at top speeds in a random direction, probably away from your target and likely towards space. In top of it, the unequal force probably breaks your lump into several pieces, each of them pushing the others away with their explosion.
In short, maybe 90% of your hard-earned antimatter ends wandering aimlessly through the Solar System. You got a pretty decent explosion at your target, that is true, but 10% is a terrible efficiency for something so expensive, and probably there are better alternatives.
Government Does Its Job!
The containment answers, IMHO are the best, but in addition:
Anti-matter may be relatively abundant (relative to what, BTW?) but government controls all the sources. It can only be used specially licensed and trained individuals. So for government-controlled ships (e.g. military) that's fine, but for civilian ships, a government-appointed supervisor must retain control of the anti-matter reactor and its transport / storage units.
At the same time, a counter-terrorism organisation exists to root out anyone who may have the intention or attempt to get hold of some and use it.
So now it could still be used as a weapon, if there was any sort of slippage / corruption / hijack or something, but in the same way a car or an aeroplane could be used as a weapon in our time. (Most people in our world have access to a lethal weapon and yet deliberate car murders are very rare - the vast majority of people just aren't that evil)
It's all well and nice that anti-matter exists, but because it reacts with any and all matter - your own ship included - it's nearly impossible to effectively weaponise.
Interstellar groups have conducted tests with anti-matter bombs, only to find that if their torpedo bays get hit during a firefight, anti-matter containment breaches and a massive explosion results destroying the entire ship - just like sailing ships with gunpowder.
The amount of cost, armour plating, containment, secondary containment and failsafe systems required to prevent this occurring is prohibitively expensive, and if you're putting that much money into containing anti-matter you might as well turn it into a reactor and build a ship around it.
After all, even if the reactor wasn't anti-matter, if it got hit anyway you're pretty much dead in space.
Antimatter container are big and heavy. Lets make them 1000 tons and 10 meters in diameter. It is not a problem to put something like this on a a big ship but impossible to use it for terrorism. It is impossible to bring something like to to planet in secret. Also you can scan for 511 kev photons that every not perfect antimatter container will be emitting.
Artificial Custom-designed Normal-Space Degradable Antimatter, stored in Special Exotic Strange Field Generator Containers
An artificial custom designed form of anti matter which is unable to exist outside of the exotic strange field generator storage containers, which are also custom designed to match specific batches of the custom antimatter.
The antimatter degrades nonexplosively whenever the field ceases as it is designed to do.
The containers draw power from the internal store of antimatter, and contain numerous mechanical and computerized failsafes designed to detect any abnormality in excess or deficit of normal operation. Any exceeded or insufficient parameter cuts out the field generation, such as excess input, insufficient input, up to and including tampering or even excessive scanning of the device.
Not absolutely 100% foolproof, but pretty close.