All versions since SH3 have had names applied to the listing in the Roster file for the ship type, but they didn't work in SH3 or SH4. Dan told me a long time ago that SH5 would indeed give ships names. Of course I was very excited about this, and the only thing keeping me from exploring it further is the sad fact that my computer doesn't run SH5. If that's indeed where the names come from I can edit the files and send them to someone, since I still have it on my PC, even if it doesn't run.
The biggest problem I see right now is the lack of merchant types available. I can do names for the ones that are there, but that's at most a few hundred names, and I have thousands of names for hundreds of different ship types. Still, it could be a start.