I've run a few games, and I prefer to have a very ... boring aproach to shipnaming.
Upgraded colony ships gets the name "Col [N]" (where N is my design version +1), Freighters become "Freigt [N]" (with the same logic as colony ships).
Ships designed for warfare gets a design name of "W2m1", for the first design of a small hull, and "W3m4" for the fourth design of a medium hull. (Fairly logical eh?)
Wouldn't deleting the content of the "ship" and "shiptemplate" subfolders in the savegame section remove my old designs from the game so I don't have to overwrite previous designs every so often?
(And yes, I know this has probably been answered a dozen times before ... but I just couldn't figure out what to search for)