I just wanted to post a followup: I was wrong, and the game DOES in fact support multiple skin cloned vessels.
Don't let my earlier comment deter you from experimenting.
Names aren't feasible because of diskspace issues, conflicts with the SH3 commander-assigned names, etc.
However, I also found out that the NKGN hullshape can also support the giant flags you'd see along the sides of neutral vessels. It's not perfectly accurate, but you only see them repeat three or four times. Many ships had two hull-painted flags so I guess this isn't too bad. Pack3d means it takes seconds and not days to clone merchant ships, so nationality-specific paint schemes are possible. Let's just say that a few months from now you guys will have NO EXCUSE for sinking neutral ships. :rotfl:
An example from armed-guard.com...
