The wiki is linked from in the AI War subsections of the site, I'm pretty sure. And obviously the forums and from within the game itself.
In terms of shot damage, it's just the damage that the ship does, times the hull type multiplier of the target, times any bonuses from munitions boosters, minus whatever armor the target has (including the armor boosting in that). There is also a minimum percentage of base damage that the incoming damage can't drop below, but I don't remember what exactly that is -- I think it's 5%, though. There are also some other ships that use special logic for applying damage, like the implosion stuff for example, but those are unusual cases. And those just replace the "damage that the ship does" in the calculation written out above.