Battening down the hatches is fine, unless you have sprung a timber, or in the case of a vessel with power, stern glands can leak. All sorts of things happen. However the ballast that most ships need to keep them "in" the water rather than on it, and in the case of a ship carrying tall masts and rigging, to help keep it upright while under sail. Will also work wery well to take her to the bottom once the integrity of her hull is compromised.