I have two ships in my world parked separately far away from each other, they won't disappear as long as parking near the workbench area I think. I always place a workbench near my ship to repair and to prevent the ship from disappearing but I never try to leave it without a workbench so IDK if it will disappear or not.
And all my ships never move out to the ocean, once I parked it stays right there even when the big waves hit it.