I lived there so I’ve seen it. Bikes are usually locked in the neighborhoods with a lot of foreigners (Roppongi, etc), but in most of Japan they aren’t. I’ve seen hundreds of bikes parked outside work without a single lock.
I live in a more rural part of Japan where you can count the foreigners on your two hands and I find it hard to believe you can even see how many bikes have their ubiquitous ring locks[0] locked among hundreds of bikes