If a boat is safe parked or not depends a lot on the location. Some places are just bad and will destroy a boat overnight. Some places are perfectly safe. And then a whole range in between. <near lots of spawns, natural pathing leading enemies to it etc>

Test an area before you commit to build a dock, you may be wasting your time if it is just a bad spot.

Most of the time I will try to come ashore where it is shallow or a small shallow inlet so I can destroy the boat and make sure I get my materials back. Never leave a boat for very long if you have never been there before... if it is really bad you will hear it banging on stuff regularly.