The one that is closed has a big rock in it this holds the lid down which then holds the doorway open. Cross the room and go through a doorway to a room with five chests in the middle.
As soon as the sub is over it you automatically dock. Sail around X-Death X-Death Exdeath's island and locate a rocky spot on the otherwise sand covered ocean floor. This is what is left of Gill Gill Ghido's island since it is now underwater. There are three points of interest marked on your underwater map, and the one in the center marks Gill Gill Ghido Shrine. Though the barrier is now down and you can enter X-Death X-Death Exdeath's castle, the door to the main part of the castle is locked, so other than talking to Zeza Zeza Xesat's soldiers who are occupying the lower levels, there is nothing else to do here.