If its in deep water, you might not see the nails. Was there any floating wood? That would be where the ship was. Those necks destroy Karves in no time. Also, when stuff breaks, it often doesn't have 100% material. A cart takes 10 nails to build, but when mine has broken, only 3 nails drop.

Boars will attack it also I have heard. But I have seen necks attacking them most often.

A couple options to prevent this are:

1: Build stake fence all around it. I dig a channel so I can bring the boat in closer and fence it off. I even fence off the exit. Then break that fence when I leave with the boat.

2: Box it up when not in use.

3: Leave it out in deep water. Critters do swim, but only seem to go so far to a stationary item. Then you can swim out to it.

4: Build an immune harbor with earth walls out to the boat and deep enough that trolls won't go. Then only Drakes could reach it, and blobs I guess.

5: Carpet build workbenches all around so nothing spawns. Could get a raid there then, so not a solution really.

6: I got nothing. Its late here and calling it a day.