I've been wonderin about that too, but i hav no clue how you could do it.

If I recall correctly, the allocation of capitalship names is hardcoded. In the player.entity files is a line almost at the top that says what kind of capitalship names to use for that player, and the game automatically gives the names in that category to the capital ships the player builds. So the only way to give frigates & cruisers names is to all classify them as capital ships, but that brings lots of problems with it.