I have seen ships sink in bad weather.
If the waves swamp a ship compartment and place it below the "crash depth" specified in the zones.cfg file, the ship will incur damage. Crash speed in zones.cfg specifies how many hit points per second the compartment loses when it is below crash depth. Eventually, a ship in a bad storm may sink. Especially if you have a mod to increase the maximum wave size. Damage may be represented as a fiery explosion if that's what zones.cfg specifies (yes, unrealistic on a foundering ship).
Also, modders who tinker with the ship's center of gravity may cause the ship to roll over in high seas. The higher the center of gravity, the easier it rolls over.
You may want to examine that ship's compartments and give them a deeper crash depth using Silent 3d editor if this keeps happening.
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