You're in a magical realm full of magical creatures. Seems pretty bold to assume that they aren't intelligent enough to view boats as something associated with foreign invaders that needs destroyed. I mean Necks in Norse mythology are water spirits, not simple animals. Making those assumptions is like assuming you can't be possibly attacked by an angry tree because trees aren't intelligent. The Greydwarves will correct you on that mistake.

In nearly 200 hours I've yet to lose a boat to anything. If you want to be safe leave your boat anywhere set up at least a torch or campfire to prevent spawning in 20m and clear out the area. A campfire is also good because you can sit next to it for 30 seconds after getting out of the water and dry off and refresh your rested buff.
If you aren't nearby (the range you see buildings you've built pop back into existence) the entire area is unloaded and paused and nothing can attack your boat so "a wolf biting my ore laden ship into splinters while I am off collecting" isn't happening. It's only happening if you are nearby and ignoring it.
Finally never leave your boat in shallow water, it should at least be deep enough to require swimming. Leaving your boat in shallow water, especially if a storm hits, will just constantly bash your boat against the ground until it breaks.