I just chalk this kind of thing up to 'sci-fi writers have no sense of scale'. The amount of firepower being thrown around in science fiction is general is often beyond absurd. Not absurd because the firepower itself is impossible, but because the idea of defending against it is rather inherently ridiculous. WiH even makes note of it several times, like the entry for the UEF bomber saying a single one has enough firepower to easily level several major cities. With so much destructive power being thrown around in such massive quantities, I honestly can't see how even the largest and most armored of ships can survive even a single volley. I don't care how many meters of super-space metal you have, if someone scores 10 direct hits with a nuke, let alone some kind of anti-matter warhead, there won't be any 'health percentage drops by 20%' nonsense like in FS. You'd be ****ing dead, a cloud of debris, if even any of that was left. There's a reason so much sci-fi has magical energy shields, and even those don't make much sense. Even if you could do them at all (how do FS shields work? Are they ever explained beyond the most vague of terms?) the energy requirements to stop, say, a barrage of photon torpedo would be insane. This is all of course ignoring the fundamental fact that since there's no friction in space to slow things down, you wouldn't need nukes (or warheads at all) in the first place. Just take a lump of metal and accelerate the hell out of it, Halo style, towards your target and let physics take over.
But then the games would be rather boring wouldn't they?
On a related note, I doubt the ships in Freespace have meters of armor. The things are big, no doubt, but I've always found them to be treated as far bigger than they actually are. For instance the crew counts. 10,000 on an Orion? Yeah, I seriously doubt that. Or the claim that the Colossus has at least 1200 decks. I especially doubt FS2's assertion that there are 'thousands of people aboard' a Deimos corvette. Maybe my perspective is just completely wrong, but as portrayed in the games they don't seem THAT big.