You could live on the ship if you like. In the lower decks there are plenty of open top grain sacks (they are all safe storage).
The captain of the ship does not exist yet. If you do the Dark Brotherhood questline, he will appear for one of the quests. The fact that you have killed (or caused to be killed) his crew will not affect that Dark Brotherhood quest if you embark on that questline.
So. . . really the only impact is that are a few less folks on the waterfront to add atmosphere to the game, and you have unlimited access now to the Marie Elena.