Well, active hardpoints are described in the DefaultCore.txt file in Assets\Specs. The .gf file tells where to place icon holders for the refitting screen and tactical displays that are overlayed on top of the corresponding ship bitmaps, as well as specifying glow regions However, I am still concerned about adding mods and messing up the game.
For example, I just tried to add DamoclesX's Negh'Var to replace the stock Negh'Var. I was able to get as far as the MP setup screen before the game just cut off. I was not able to play any mode until I reinstalled the game. I was wondering why this would happen after just copying/pasting files into the ship model folder. even after I deleted that folder and put the original back in, I was unable to play until I reinstalled.
This example makes me weary of adding mods, but I have heard of others who have done it successfully and can still participate in MP games with unmodded players. That is what I was hoping to do as well.