How do I handle an unused light fixture junction box in a bathroom?
Since it sounds like you have a major remodel project in process you probably have all the walls open too. The very best bet for the discontinued light would be to remove the circuit and electrical boxes entirely. This way you do not need to keep an ugly do-nothing electrical box cover on your wall or ceiling. 

Keeping an unused electrical box accessible can be an extra burden if you are trying to put tile on the wall or finish a ceiling. Remove it and eliminate those PITA points.