look on ground underwater near where boat was
if it was destroyed less than 2 game days ago, its resources will still be there
if its been longer, wave bye to them

i build a nice dock and wall around boat when parked, some good protection from waves and mobs, never had one disappear since

In my latest run mobs destroyed my boat once and the second time I caught a boar attacking my boat. I'm not sure what cause mobs to attack a boat but it does happen at times.

To avoid this int he future.. run your ship aground then destroy it.. place it down when you are ready to leave.

Boats can be destroyed by enemies, or possibly by large waves slamming them into the shore. If nobody is on them, they don't move at all, though (so they can't become runaways).

Most likely you didnt place a workbench near where your boat was left, and something attacked it.