I think the game only simulates the world for a certain distance around you. If you beach the boat and then move a good distance away, it'll be fine. If I don't plan to leave right away, I'll build a staging point base right next to the boat so I can keep an eye and ear on it (you can hear the crunching sound if it's being attacked). I always leave boats beached on the shore, and only lost one twice. Both times I think I was too far away to notice what was happening to it, but close enough that it was in simulation range, where stuff can spawn and attack it. Doesn't hurt to check the boat before sleeping for the night, just in case.