How being at sea changes damage-control readiness

Would deep water change the type of damage control used?

Yes, but the larger advantage is that underway ships would already be secured and manned for sailing rather than opened up for harbor inspections.

Deep water changes rescue and damage-control conditions, but readiness also changes before the first bomb falls. Watertight integrity, watches, and the ship's internal condition would reflect an underway fleet rather than ships alongside in a peacetime harbor routine. Compartments would be secured for sea instead of opened for Sunday inspections, and more of the crew would already be at sailing stations. That higher initial readiness cannot make a badly damaged ship recoverable from deep water, but it can slow flooding and improve the response to the first hits.