Like others have said, a fair number of Japanese youth do have piercings.
However, it will be very difficult to get any sort of job with piercings. Even if the employer doesn't care, they'll still probably be worried that it might go against the tastes of the clients.

A lot of people have perfectly fine luck keeping their piercings but taking the piercing out when they go to job interviews or when they're at work.

If you're not looking for a job at all, it probably doesn't matter.

I studied abroad at a university in Japan last year, and trust me, the university probably could care less. I've seen Japanese guys that look like they belong in 80's hair metal bands...It took a LOT of bleach to do what they did to their hair.:D