Let me make a note to see about adding a "manufacturer" field to ships/weapons. There's only so many cool names, especially the more obvious ones, so I think any attempt to have mods not step on each others' toes is... well, depending on the total number of mods, it's going to be less than practical at some point, and people are going to be unhappy.
IMO, if mod ship/weapon/etc names clash, either with each other or with vanilla, then that's just a thing that happened - regardless of who had it first, I don't think it's fair to expect someone to give up a name that fits whatever they designed and is thematic to it.
So for example if there's a BRDY Scarab and a Nomads Scarab (which is very thematic for Nomads in particular), I don't think that's really a big issue even with vanilla having a Scarab. Especially if there was a way, in-game, to tell where it came from.