There are many small islands and outcrops of rock protruding from the seas surrounding Japan. They cannot be crossed, it is necessary to carefully row around them. They can be fired over, depending on the size of the ship in question and whether there are archers on board.
Coastal areas and islands may have areas of shallow water nearby. Your ships cannot cross shallow water for fear of running aground, it is only possible to row around it. It is possible to identify shallow water by the dark rock patches or coral reefs under the surface when near a coastline.