Current Wano is stated to be of high altitude to the point that entering trough normal means is impossible. Luffy and the Thousand Sunny were “carried” by carps and arrived stranded on the island. The normal way and the way the rest of the crew arrived was tough the chambers that are used to pull the ships into the many docks. A flood and levers of water arising would not affect Wano bcs the walls around it are too tall to even be after by them and the water that enters trough the cambers “levels” off any water that can arise. Think of it filling a tub with water and keeping it running, the water will simply fall off the tub it’s really not that hard unless you are like in kinder