Ship damage (when not the result of hitting rocks) in my experience, is gradual over time regardless of the weather or wave action. It is almost like it is timed to happen every 10 or 15 minutes. My longship takes 10 damage regularly whether I am in stormy or calm seas. It does damage when travelling at a high speed when there are large waves & rough seas waves, when the ship goes somewhat vertical getting air between it and the water, but apparently that type of damage can not trigger more than once every couple of seconds.

I only ever sail the longship. It is definitely the most stable vessel, it is easier to handle and can take a lot more damage. I always make sure to moor it in shallow water, if I am going to break it down, or if there is a chance for it to be destroyed by enemies. Sometimes I will moor it in deeper water off a small island, well away from shore, but generally I will always find shallow water. Now that loot and items float, losing parts in deeper water is not an issue.