That's a good point about masts and sails. At the moment it's actually supposed to work the way you say, but I haven't tuned the probabilities well so things seem to break straightaway.
Waves already move the ship, at least in a simple-minded way through buoyancy. The flooding system I want to implement would be something like - when the local height of the sea is above the hatches or whatever, then you take on water that can sink or destabilize you. Is there some other mechanism that should be happening if you are struck on the beam?
Detailed coastlines - maybe. Right now Portsmouth harbour is just a 3d model loaded into the scene. Issues come with when you need a different style of rendering for it (say if it has trees) and how to deal with level-of-detail and time compression.