Several times I have had boats despawn in the world, 

1, whilst I was getting loot inside sunken ship, jumped out of boat went down to ship returned to surface and boat was gone,

2, jumped out of boat next to river bank turn around to break the boat and it was gone,

3, slept in bed next to boat in the river, when left bed the boat was gone,

I have noticed that the boat seems to dissapear then reappear when u jump to exit,