I lost my first 3 boats. I thought it was a glitch, until one day I parked my long boat off shore and swam. I was actually in black forest (close to the plains). I had to swim to shore.
I was on shore maybe 15 seconds when I heard a "Smash" I stopped... heard another "Smash" I run back to my boat and a gobby is beating on it. I couldn't manage a shot w/ my bow and my ship was destroyed.

If you aren't finding any floating debris... then perhaps there are some shenanigans going on.

But I haven't lost a boat in weeks.

All my boats are now secured in docks. I make a dock, make it width of 1/2 core +1 full core beam and your boat will fit perfectly in that. Build walkways on either side, and secure the boat once its in by either placing doors on the side or small wooden floor pieces. It will hold fast.

For "Assault Landings" (especially on plains) Swim. Make sure you leave yoru boat off shore a decent distance. Then I drop camp fires all around the beach head so nothing spawns around my boat as I leave it or approach it (or loiter around it).

Once your boat is no longer in the zone you are loaded in... nothing can happen to it. Its when you are "nearbye" but "out of sight" when bad things happen.