Firstly, boats don’t drift off. Once you exit them, they stay put.

Second, the water will move up and down, so if the water is TOO shallow you will gain damage from hitting bottom.

When I build a dock, I dig it out on tippy-toe until I can no longer touch bottom. That is not so deep that you cannot recover materials and deep enough not to hit bottom.

I never worry about holding the top of the ship down. Frankly, once the storm is over you will take a little damage from rubbing against the dock, but one swing of the hammer will repair it.