I'm actually going to have to mirror what Swiss just said.
I can't really see this RP working with smaller ships at all.
Smaller ships just... they just wouldn't work.
That said, you're going to have to keep your RP brilliant and inventive to dodge the "OMG PVP LOLSAIR CAPHOAR" tag that is wantonly tossed around here.
You don't necessarily have to kill people to get their souls.
What about trying to take pilots? Tricking people into joining your crew?
Watch pirates of the Caribbean Two, some of those old ghost ship movies and things like that to get some ideas.
As for other RP ideas... You're a ghost ship. You shouldn't really be seen moving about - you should try to stay as hidden as possible, and as far away from anyone as possible until you strike. You could do some interesting RP along these lines. You could try sneaking up on people through nebula while being creepy with RP while attempting to herd them towards you by making them think you're behind them, etc... You could lure them into the Eta minefield and trap them between your ships in the passages... something. Use your head.
There's a dozen and one creepy and less-than-malevolent things you can do with a ghost ship. Obviously, you're going to run into combat with them. But you should try to freak people out by skirting clouds and staying off the plane and just in site whilst RPing creepily and mysteriously.
Perhaps the best thing you could do is instill a sense of foreboding in people, hint at things that are to come, etc....
You don't have to tell people everything, nor should you. You can reveal a little bit at a time, you could be cryptic like the Keepers. Each ship could have a different history that plays into why it goes where it goes, and why it hunts who it hunts.
Maybe you could even RP past scenes of interaction between crewmembers, or the last battle they fought in, or refer to events that happened years and years ago. If you seem to be stuck in another time, that's a bit more creepy.
Again, you should definitely be mysterious.
That's probably the best key to your RP.
It shall take a good deal of work, but I think that it could be pulled off in the end. And it would be awesome.