Part of the problem is in the waves themselves - the period (distance between crests) is too short. In real live any ship will "go green" (plow the bow under) if the sea is heavy enough, but usually the waves are far enough apart that only the bow will go under. This may be amplified for a deeper-sitting vessel like a submarine, but you're right - it's a bit much in the game.
One side-note: A long, thin ship like a destroyer will have more problems in heavy seas than a short, stout ship like a corvette. The smaller the ship, the less likely it is to get swamped. In the game it's just the opposite. Little ships are always sinking.
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