EDIT: 2GT nukes are commonplace? Screw big ships
Especially in case where each of those small ships can carry and is actually armed with a nuke or several of compared yield. And especially if manufacturing a 2GT nuke costs hundreds of times less than bulding a 1200-meter long spaceship armed with "conventional" weaponry, like lasers, kinetic stuff and ordinary missiles. When you devise a war of this scale, you are playing a war of attrition already, and having a nuke of that size declared a common weapon does put requirements on what could be effectively fielded against an enemy armed such.
Compare Earth, fleet battles with expected nukes. A sizable fleet travels in a very loose order, so that if a nuke is detonated over it, only the closest ship (or the carrier, if they have one in the fleet, as they are actually very vulnerable) will be destroyed, the neighboring ships would likely survive, and the majority of the fleet would only go on high alert (and probably help the crew of those less fortunate). While creating a single nuke costs about a thousand times less than building a battleship, the delivery vessels have to be included into this cost together with the chance of all of them to be destroyed, this makes the cost of actually delivering a nuclear explosion to a fleet be comparable to one ship's worth of money. Also the aftermath of blowing up a nuke is a part of cost to be paid by either party over years to come, even if it's blown up far from any shores, this part of cost acts as a detriment to ever use them in the first place, and is not present in space. Even so, using nukes en masse vs fleets is considered cost effective.
Now, project this to space: first you've got a 1200-meter extremely expensive warship, armed to the teeth, then you say "there are nukes of 2 GT that can be launched as a salvo". As pointed in the answer with maths, a close hit of a 2GT nuke obliterates pretty much everything (although I still claim the below points would help that ship to survive even that blast), but even if the ship won't get destroyed right away, it would still be badly damaged and have to be taken to repairs. So, one nuke = one ship, maths really can be this simple. They spend one nuke, you spend one big ship - so the best action will be to not field such ships vs such nukes. In case we still count those nukes that fail to reach the target, there are tactics that couldn't be done in oceans that would allow overwhelming the enemy point defense at less cost than delivering a hundred warheads, say plain inflatable dummy shells that produce the same kind of radar footprint as warheads - you can't go easy on Earth due to atmosphere (although ICBMs do have such decoys while in space). So while the enemy would have to spend a dozen actual warheads to ensure one close blast vs point defense, the costs are still in favor of nukes here.
END OF EDIT
PS: building layered nukes, while possible, also increases their size, remember the Tsar Bomba was "mere" 100MT yield as a project, and was some 2 meters across, meaning that a 2GT nuke is no longer a target for just point defence systems, normal weapons could be employed to try and blow it up before it'll blow up the ship. So a part of the answer will be "blow them with your main caliber", for example, a single nuke blown up in a field of decoys would eliminate all of them, and might even set off an enemy warhead, which might then turn the costs war in your favor.
Layered anti-dust armor
In fact, nukes in SPACE are overestimated. The largest damage dealer with the nuke is the shockwave, and if there's nothing to shock with, this kind of damage is mostly mitigated. So, you have your armor layered like modern day's Whipple shield, a couple meters deep, with some defense systems showing out of the topmost layer to actually do their job (remember ye olde Doom Star), this way if a nuke (of earthly size, averaging 1Mt) would go off at the surface, the layers would sequentially reflect some of the direct radiation away from the ship, as well as cause the majority of EMP energy to be caught into heating itself, also preventing the bulk of armor to get insta-vaporized. It will still do damage, but with several meters worth of ablation it might not be as devastating.
A nuke worth 2GT blowing up at 1km distance vs such a shield would still cause inward momentum, vaporization of a part of hull, shockwave hit from the ship's own ablated armor turned plasma, etc, but this armor design still comes up on top versus solid steel. First, its layered structure also acts as a shockwave damper, absorbing shockwave energy by breaking apart at depths not vaporized. Second, solid steel does not reflect energy as good, especially penetrating radiation, while every exposed surface of layered shielding would also cause a bit of reflection. Third, when the nuke would turn outer layers into plasma, it will initially have less density, as there is vacuum between shield layers; thus the process of the blast energy penetrating the defense layers would cause more energy to be absorbed by plasma than in case of solid steel wall. The major result would be more plasma heated by incoming radiation, thus less steel vaporized, this will also result in less momentum delivered to the ship via ablation recoil.
Kinetic shrapnel point defence systems
Lasers in SPACE are also overrated by a great margin. Lasers have the most damage dealt at the source, regardless of construction and/or distance to target (mitigated by cooling systems, but still), while kinetic weapons cause direct hard damage to whatever they hit, also their construction can be made to lessen the initial damage to the ship caused by acceleration of the kinetic projectile (railguns etc). Even ancient era machine guns, if fired at an incoming nuke (it's detected at enough range to aim the guns), would cause enough shrapnel density to guarantee at least one hit, and with delta-V of those ships a single bullet hit will be enough to disable an incoming nuke outright. A gas-powered shrapnel cloud weapon with initial particle speed of ~200 m/s would cause more than one hit against a standard-sized nuke (2 meters diameter), and would cover the area of more than 100m in diameter after half a second from launch, more if projected forth on top of scattering. Use several of these in general direction of an expected incoming nuke and watch it get shredded.
There is a tale about Soviet response to US's idea of laser-armed satellites, where the Soviet chairman replied "We would just launch a bucket of nuts and bolts to a retrograde orbit, your laser things would break apart". The general principle would certainly hold itself in your space conditions. The funniest thing about such a defence is that the shrapnel cloud could have zero relative velocity to the launched ship, but if it'll be dense enough, it will destroy any incoming device that's more complicated than a rock. And if you have some small control of gravity, it's possible to devise a protection system that will launch such a cloud in case of incoming nukes, then collect it back once they all got eradicated. (As a side note, such a cloud would also destroy any decoys as well, so devise a projector ship that would be able to whizzle around your fleet and poof shrapnel around itself to catch stuff flying your way. There was even a real life project of a space ship, Project Daedalus, that had such a protector ship flying before the main vessel in order to protect against space dust at high speeds.)