Originally posted by Weaver:

As long as its not overly shallow water its fine. Also if the chunk its in isn't loaded from a player being near nothing can happen to it as an area not loaded is paused till a player gets near (aside from stuff on timers).
Waves only move the boat up and down, not side to side.
You can also take it to shallow water and axe it down to its parts.

This is correct.

The boat does not move (besides up and down) when no one is on the boat. You can even stand out of the boat and interact with the storage and the "full physics" of the water will not take place. It will not float away.

In bigger storms, the boat may hit bottom or rocks beneath it that can cause damage. Overall, I don't think I've ever had a boat destroyed from just sitting there. If anything, I've had boats destroyed because I didn't clear the area and some enemy came by and just whacked on it. So now I always build a wall around the boat when I want long term storage. I've never had a boat destroyed that was walled off.

Sure, you can destroy it and save the resources. Or you can have a cool looking boat sitting in a cool looking dock.