I don't know, pretty much everything has that single upgrade that really makes it sing in stripped-down roles.
CR90A - TRC
CR90B - SW7 or title (depending what you want it to do)
NebB - TRC or Yavaris
GSD - OE
RDR - OE
MC30T - OE
MC30S - OE or TRC
Certainly, people have done the run-naked thing successfully (naked AF-AF-CR90 at Worlds last year), but you're really building for a specific tactic if you're going to be doing that. I think that in most cases it's worth spending the small incremental price increase to put that single upgrade on your almost-naked ship.
All true, however once the points become an issue, using naked ships can be a valid option (and for cheaper ships running naked means less points to opponent once they're destroyed as was already noted).
I think another candidate for running naked is RDR2 in a role of flotilla hunter.