Wiping the folder should be sufficient. However there is another folder which holds ships designed in Metaverse games. Also, any time you load a game and then save your progress, ship designs will get saved into these folders.
What this means is, if you intend on playing more than one game at a time, use different ship styles for each one, as designs which use a different style than the one you're playing as will not show up. You can see this in the filenames used for the shipcfg (which tell the game which part is connected where among other things) which start S0_, S1_, S2_, S3_, S4_ according to which style was used to make them. Thusly, you can remove just those ships when you end a game using those ships.