It's likely that until he is released from prison he will be considered as part of the Navy. He will likely be dishonorably discharged once he leaves prison but he will continue to receive medical and welfare check ups until he is discharged. I know a guy who used to have to go down to Mexico to check up on some Marines who were incarcerated there for big crimes (I think they murdered a prostitute IIRC). They would bring a Corpsman or doc with them to provide medical care and commissary goods to them (blankets, clothes, food, etc.) since Mexican prisons require families and friends to provide for the prisoners. They may also work out a prisoner swap and move the dude to a brig. I've heard of that happening before. I assume that will be worked out between the US Embassy and Japanese Government. I'm sure there are a lot worse places to be locked up than Japan.
I wonder if he had been diving prior to the high altitude exposure. I've heard of similar things in my scuba training. It happens among high altitude divers and for those who ignore decompression times prior to flying or other low pressure environments.