OK, I've read that ships disappearing was an issue for a while, because seagull landing on it seemed to carry them away (because the ship was seen as part of the seagull).
I think I'v seen a fix for that in a changelog, though I can't find it right now....

Lately, I was jogging along my dock, where my boats are moored finding my karve missing; it was not destroyed (a workbench nearby, no material in the shallow water), it was just gone....

Found myself a bit like Captain Jack Sparrow at the end of PoC III...

Are vanishing ships still an issue? Is there a way to prevent it from happening (other than destroy the ships in shallow water to store the materials)?