The bigger problem with the Tokyo-Okinawa route as a hyperloop candidate is that Okinawa is an island far away from the main islands of Japan (kind of like Hawaii). Not a great candidate for land-based transportation.
Well, actually that's not a massive problem. The spans between the individual islands isn't huge. The longest bridge in the world is 164km long and built for high speed rail.
The issue is Japan is earthquake prone, and big bridges in tsunami areas is probably a bad idea.
