As a first little step to bring them back into the game, I've found a small code segment in trek.exe, which controls the maximum number of damage textures per shipclass (usually 12 for the vanilla ships). Its located by the phaser slots and is 1 byte long (here the vanilla Sovereign):
Trying to set this the value higher than 0 by the most of the new ship models will crash the game at the moment the model is loaded. However there are some ships where this does not happen. At least not immediatly. In my case there were 2 cardassian models (kirol and gildron), which could be loaded with enabled damage textures. Unfortunately the game crashed in that moment when these ships were hit by enemy weapons with this entry in crash.log:48 48 33 00 04 00 00 00 01 00 00 00 10 00 00 00 00 00 00 00 0c 00 00 00 00 00 00 00 66 66 26 3f 1a b8 19 11 11 15 14 16 28 29 29 21 21 25 25 24
Possibly more investigation in ship models like that, which don't let the game crash immediatly could be useful to solve this problem and let us find a way to add the damage textures to the new models.ST:BOF Wed May 26 00:56:41 2010
Version Under Test: 72
File: object.cpp, Line: 495, slotNumber <objData>TotalObjectSlot
Initialize State: 31
Player Empire: 0 Starting Seed: 1274828025
Galaxy shape: 1 Galaxy Size: 0
Turn State: 20
Turn Number: 10