Leaving an unattended boat has always been an issue, which is why many players have adopted the practice of breaking down their boats (in shallow water) to get all the parts back, and either put the parts into a chest or carry them until ready to deploy the boat again.

It's also good practice to place down a portal anytime the player reaches a far away place, especially after a long sailing voyage, or anywhere that would be a real pain to travel back to, in case of death.