savorysashimi: I, too have this issue. Thankfully, as far as I know, all (notable) Black Ship events are actually inside the ship (not on deck).
If you want to access the inside of the ship at night, and it happens to be night, sleep until tommorow midday/evening, board the ship, go inside the ship and down to the sailor sleeping quarters (the room with all the bunk beds). There, you'll find a place to rest until nighttime and access any night missions inside the ship.
As a side note, even doing all that, you still won't be able to access the deck at night this way (from inside the ship) either, but as far as I know, you shouldn't need to.
But, yeah, it shouldn't do that. :) It'd be nice if they fixed that so we can see what it's like on deck at night. I hope they get around to fixing it.
Thanks for the heads up! I'll give it a try in my next playthrough, after seeing whether it crashes during the day as well.