Yes, its one of those. The question is simply this.
How do I edit the names of the ships? Is there a file with a list for the names of ships?
Yes there is its called and odf file. Just open the file for the ship that you want, scroll down untill you find "PossibleCraftNames" and edit as you wish.
C:\Program Files\Activision\Star Trek Armada II\odf\ships
Oh, and no question is stupid, check out westworld's big book of modding for further info.
Also, theres a list of 1500 ship registries (names) available for download over at a2files for you to use if you like.