As a night-stalker player, I agree. It’s entirely acceptable and understandable if night-stalkers simply don’t have a place.
It could be cool though. There are many monsters and legends at sea. The terror was a kraken like thing, surely something like that was actually a night-stalker thing giving the kraken a bad wrap? Something like sirens that draw ships into terrain? Groups of soulflayers that fly around; are hard to hit, board ships easily, but can’t take much damage.
Getting a game established before adding the faction of weirdness is probably best though.