this is easy to reproduce. play a game, design ships give them your usual names. then, the next game you play, do the same thing, ie use those names that you usually always give to your ships. if the name has already been used in a past game and GPF. i keep telling myself to lower the autosave delay so i can recover with the least loss and i keep forgetting to do that.
this just happened recently, and went to the user data folder (my docs/my games/galciv2) to delete the custom ships file.. reloaded my autosave, and all the files re-appeared, so i'm guessing the ships are also stored in the save.
therefore to get rid of this problem, delete your ship files, start a new game, and remember to delete your old ship designs instead of just rendering them obsolete