My problem is that my sapphire and ruby there internal battery has run dry. I just want to find out if I would be able to still get a master ball in the game like normal. Also where do I find them?
Yes. You'll be able to find it in a room at the Magma or Aqua Hideout after Mt. Pyre.
It is in a room in the Magma/Aqua hideout. You need to teleport using the portals on the floor to get there. Watch out, it is near Electrode.
This video will help.