Sorry for the necroposting, however I found that is actually possible to eliminate the ID code the game attaches to the name of your custom designs.
You need to open the console and use the command shortshipnames, this will eliminate the code (however this also made possible to overwrite your designs - for instance, if you create a ship and call it "Battleship Alpha", then create a second ship and give it the same name the new ship deletes and replaces the first one).