Acceleration depend on Thrust to Weight Ratio (TWR, examples)
- Merlin 1D rocket engine, full-thrust version - is capable 1765 $m/s^2$ , but it does not include mass of fuels and rest of construction.
Second limiting factor is ISP (and power generated) - which determines needed amount of fuel to achieve desired speed.
There are fuel less acceleration system, for example, solar sail like solutions and acceleration thing with laser - where just flat mirror-like surface may act as engine - it will have high ISP but also have some TWR which depends on perfection of the system.
Close to 1 c in one hour is pretty high acceleration about 80000 $m/s^2$ or about 8000 g - it is high, but not astonishing high even for ordinary materials (this depends on the form of construction). (As an example, 0.1 x 0.1 x 0.2 m piece of steel (2L) first liter of steel will press on second liter of steel with force about 56 tonne, whole acceleration force is 112 tonnes - this form and material is perfectly capable to withstand that force. Sure such bar of steel is not a rocket, and rocket with given acceleration rate will make hard times for developers to figure our how to build it).
Tactics
Sad but it needs to be said, but you started on the wrong foot.
First of all you should think about tactics and what capabilities you have.
Missiles will be always capable for higher acceleration rates than ships, not because of humans, but because it may have no payload except engine, fuel, energy source, where ship should have all that and payload - humans, cargo, whatever. Missile be faster than ship is actually all you need in general. Antiship missiles are not the fastest of their kind, they are just enough fast for the task.
One hour to 1 c speed means actually an acceleration distance of about 540'000'000 km or 3.6 AU. - I personally find such combat distances pretty realistic, but what about the ships? Are they capable to break the distance? I guess not, but depends on the tech, and how prepares they are against attack and their goals. If not, nothing significant will change if you will hit the target not in one but two hours from four times of that distance. It may make no sense, but this point will be dealt with in next paragraph.
If you rely on speed of the rocket as means to protect it, and make harder for attacker to defend against it, there is a problem - it is not so simply. Thin foil around the ship, let say few light seconds around the ship - will effectively protect it from 1 c projectile, from any direction.
Big enough gas cloud (balloon or just a cloud either from the blast of antimissile's rocket exhaust or by exploding it (as example)) may act as effective countermeasure especially if you know the approximately direction and the time of launch of the attacking missile. (There are countermeasures for missile in that situation, but there are countermeasures for countermeasures.)
And for reasons of how thick should be that foil around the ship - thickness of it grows proportionally as the square of speed (proportionally to kinetic energy of projectile). For example, if foil with a 1 μm thickness is enough to destroy the projectile at 0.9 c, then it have to be 100 times thicker for a 0.09 c projectile and this means 100 times more mass for that shell and this may make this sort of defense ineffective. This is an example of how lower speed may affect defense strategies making it more complex for defending vessels. Yes, you may have difficulties to detect 1 c projectiles with your systems, but you do not have to detect them to be protected against them. Lower speeds of projectiles allows the use of detection systems but what it actually means is replacing a simple at-all-times working solution, with a more complex and less efficient solution (which may not work).
There is delicate balance between many of the factors, and depending on particular implementations there may be some local optimum for speed differences between the target vessel and missile, but it is not necessary have to be 1 c velocities, and most likely not for ship-to-ship combats at multiple AU distances.
How big the ships are is actually not very much important, as far as with their sizes - missiles and defense systems scale proportionally to the mass of the ships.
There is an example of an attempt to model possible tactics for combat in the solar system. But if you prefer combat in interstellar space it will work in a similar way just replace the star with a ship and adjust scales to match the sizes. (detection and countermeasures swarm shell may be still light hours around a ship)
So I recommend starting with combat tactics, with the ships' characteristics, with the nature of the space where the combat takes place, and with goals of defenders and attackers.
The nature of tactics is very sensitive to details, the slightest change may change the whole picture, it means you will never have to guess, but even beginning with guesses, you have to define a lot of the details. More details you have defined, harder it will be for your opponents to prove that one is wrong. :)