About police checks, I've been asked for ID four times, however, coincidently, twice was one day, and twice was on another. Here's a breakdown, judge for yourself if it looked discriminatory:

First time: I was lost in a neighbourhood so approached two police officers asking which way a certain district was. They saw that my bike didn't have a lock and, after helping me with a map, asked for ID and registration details.

Second time (same day as first): Five minutes after the first time I cycle around a bend, and am them pulled over by two police and asked for my details.

Third time: My (white) girlfriend and I were riding into town. We stop at some lights where a policeman happened to be standing. I get asked for ID and registration details because of my bike having no lock. My girlfriend doesn't get asked.

Fourth time (same night as third): I'm riding home, a little bit drunk, maybe going a little bit fast. Two police officers pull me over and ask for ID, then do a full check, asking where I work, how long I've been in Japan etc, writing it all down. They said I was riding my bike recklessly and to take care on my way home. On my way home I see police EVERYWHERE stopping cars and doing checks. It was quite bizzare.