Now I'm not one to understand explosion physics in outer space fully, or even normal explosion physics, but I have a hunch that the force exerted by the explosion would be affected by space in a way that would favor the person being shot at.
AFAIK, most of the damage that comes from nuclear bombs of today come from either radiation or the shockwave. IIRC, the main explosion, while big, is relatively small compared to the affected area. The nuclear devices in WWII were also detonated IIRC above the surface of the Earth, so the shockwave would affect a greater area. In FS2 however, the missiles detonate upon impacting the surface of the hull. I'm not sure how much that would affect the damage of the warhead, probably some.
Shockwaves by definition are energy carried through some medium, and thus either space in FS2 is filled with some liquid (that'd explain sound too

), or the shockwaves can't exist, although the bomb shockwaves only tend to support my "liquid space" hypothesis. Come to think of it, liquid in space would allow beam canons to work, as well.

I am thus forced to conclude that the armour and sheilding on the spacecraft are excellent means of absorbing damage.