Whenever you're in the vicinity of your boats and buildings and objects are loaded in, the boats become prone to damage sustained from colliding with them. This happened to me a couple of times, including their materials vanishing, so I guess the same is happening to your boats.
You mention having stone walls built around the boats and having poles and stakes placed in the water, likely to protect the hulls. Perhaps the masts are still able to hit the stone walls or poles whenever the boats rock on waves created by storms. This results in damage over time and can even sink the ship when sustaining too much damage this way.
I assume that materials vanishing is due to the new coding that unloads unused assets. They likely erase the ship's construction materials when they aren't near workbenches.