There are no hidden dungeons for chapters 3 and 4, though there is an "alternate history" dungeon for chapters 4 and 5. The Japanese wiki says that there is a hidden dungeon for chapter 5, but I haven't figured out how to open it. It looks like it's something about the port, but I don't see it with my port at level 51. It might not be available yet.
You will have to swap out generals as you get better ones, but it's easy to transfer gear to other generals.