I agree. Ships of the damned are poorly implemented.
1. They should be persistent on the map.
2. Not spawned the same way mobs spawn.
3. Visible from much further out. (IE shadow LOD like islands have) in fact, all ships should be visible like islands with a shadow LOD.
4. They should act like a World Boss.
At the moment rather than implementing them better, they are just being nerfed into the ground.