Yes, it seems that I managed to get rid of the damaged texture problem! The ship takes damage from deck gun and torpedoes and I've even seen deck gun make small holes to hull below water.
Okay, let's see if I can explain this, i'm a bit hangoverish...
There was a two or three materials (type 2/0)set in S3d but they seemed to be empty. I followed what iambecomelife did with Salland-ship (thanks!) and gave the textures a name and then embedded a targa image below that. And it did the trick!
So the ship needs still following things: crew, Sh5 wakes, water reflections, maybe the normal map thingies. And I'm not sure if it's working properly, at this point it looks good though. Phew!