When it saves a ship design, how about adding a subfolder under \my docs\my games\galciv2\ships\ that corresponds to the different race styles? That way, if design an Altarian-style ship, it goes under \my docs\my games\galciv2\ships\altarian\.
If I play with a different style in a later game, the Altarian-style ships will not appear, but I can't create new ships with the same names. If it only searches for player designs in the race-specific sub folder, that won't be a problem.
Or, eliminate the character limit when giving a design a name? The limit is annoying anyway, and getting rid of it would let me specifically name the race that the design belongs to and not confuse the game (or myself) later.