A brief sci-fi rant. You all seem to be going hard towards the realism aspect. Given the nature of this topic I think it's important to bring this up.
http://www.youtube.com/watch?v=1HYhXzN-opo&feature=related These are nukes in the 50s-60s. Based on the figures demonstrated in the video, such explosions create novas which expand and engulf the entire FS2 'mission area'. Given 24th-25th century weapons technology explain it how you will, be it some kind of antimatter thermal quark subspace rift blast from the manifold plane resulting in an electromagnetic plasma flux vortex of entropic chaos etc, I would imagine that the areas of effect would be much greater and much more destructive.
'Going nuclear' does not seem to have any moral implications in space, so from a realism standpoint, it would make sense for weapons to have a much wider blast radius.
There have been explanations of how capital ships would get away with surviving indirect impacts from weapons of mass destruction, nano polymers, active armor, or good old massive sheets of steel, but It does nothing to explain the impressive visual impact these bombs would have.
The way I try to explain it away in my head so it does not bug me in the game is that future space based armor is so advanced, yes an unshielded fighter can resist a nuke, that any meaningful destruction requires very focused energy distribution of warheads, and that a wide blast radius is a 'waste of energy'. 24th century weapons channel their energy (somehow) into a small area, but they are extremely destructive. This still does not explain how Shivan fighter shields are so resilient to anti-capital ship warheads and why laser turrets are a better bet. I remember volition trying to explain the UD-8 Kayser as having some sort of wave diminishing effect on Shivan shields by cancelling its electromagnetic waves crest meets trough style.
I guess at some point you can say, how dare you impose boundaries on a society that broke the fabric of the cosmos? Just like trying to explain the idea of a jet bomber to a medieval man. "It's a flying castle that drops fire!", "BUT HOW?!" gaps the medieval man. I'm sure at some point 21st century science would be hard pressed to explain 24th century technology.