Undoubtedly part of the reason there aren’t many racers is because motorcycle usage is pretty rare. You find scooters all over the place because the license for that is a breeze. Well, it’s the same as getting a car license, since you’re allowed to ride a 50 cc scooter with no other qualification than the regular driver’s license. There are no provisional licenses in Japan; the earliest you can get one is 18. Most young people don’t bother because unless you live in the country having a car is silly when public transport is convenient and cheap, and having any kind of vehicle is expensive. I have to drive, and it costs me over US$2,000 a year just in taxes of one kind or another for a regular old car.
Getting a mid-class or higher license is a royal pain in the ass. There are small, medium, and large categories: 50–124 cc; 125–399 cc; and 400+ cc engines. Getting an open license is very difficult because I’ve heard that they actively look for excuses to fail you. In the normal test they’ll make you do things like balance on a 30 cm wide raised section for several meters, and you lose points if you go too quickly (speed helps balance through gyroscopic effects). Set a foot on the ground there, automatic failure. You have to go very slowly across an uneven pitch (description here) without dropping the bike or screwing anything else up. Or going faster than the tester thinks you should.
Oh, and you have to use their bikes, which you definitely aren’t used to. Have fun trying to pass when they routinely fail 90% or more of the people in each group, sometimes just on basic principles.
In addition, up until very recently (last year I think) you couldn’t carry a passenger on any high-speed roads. I use the term high-speed loosely since speed limits are usually a max of 80 kph (49.7 mph). Vehicle taxes are based upon engine size, so a big bike could cost around ¥30,000–50,000 a year in direct taxes, with inspection fees running around ¥100,000 every two years. A last point is that Japan’s climate sucks for riding. I had a motorcycle as my only form of transportation for a year and a half when I was living in San Diego. It was sometimes hot, but not the heatstroke-inducing muggy crap that you get in Japan. It got frosty, but not icy, sleety nastiness like most of Japan gets during the winter. If you’re lucky, you can ride one for about 3 to maybe 4 months of the year. The rest of the time, you’d have to be nuts or a glutton for punishment.
All of this means that there are few people with motorcycle experience, few role models around (no Hell’s Angels, no cool high school kids with crotch-rockets and leather jackets; they tend to be middle aged guys with the cash to spend on expensive toys), and few situations to make young, stupid guys dream about going really, really fast. I’m not really surprised that there are very few Japanese riders around at all.