Having lived there for a while and checked out a little bit of the racing scene, I have a few guesses.
Basically I think that bike racing is a severely limited career option in Japan. Japanese society is extremely rigid for the most part, and going against the prescribed order of things is sometimes difficult or impossible to do. For instance, in Japan schoolchildren take entrance exams for highschool, college, and for jobs. These determine to a large extenet how far one can go. And, missing out on taking them at certain age levels can really set one back. I think a lot of potential riders are forced to worry about school and jobs rather than racing. If you want to make bike racing a career you really have to make it your career and go all out. Nakano for instance chose to go pro instead of finish college for engineering. Had he not done well with racing he'd be in a bit of a spot trying to go back and finish college/find a job. Companies would be asking why he's doing it so late. It wouldn't be accepted.
Also, the Japanese national superbike series is pretty weak overall. It doesn't have the following that US or European series' do. As such, there isn't much money being thrown around. So again, not a very attractive career choice. You'd have to hope to be scouted and "adopted" by one of the big factories in order to make a go of it.
It's kind of surprising really. Pocket bike racing for little kids is really popular. They seem to get started at an even earlier age roadracing than kids in other countries. I think societal/educational pressure pushes lots of kids out of racing, or just makes it into a hobby for a lot of kids.
As krazy said, it seems to be kind of a weekend warrior thing. Lots of trackdays and amateur series stuff, but not many pros out there.
Thats my take (guess) on it.