I used to cycle everywhere when living in Kyoto in the 90's.

When taking JAL out of KIX I normally parked the bicycle in front of a Pachinko joint in front of Kyoto station before heading for the Haruka. Don't know if it's the usual police-yakuza symbiosis but it was always there even after a weeklong trip. Elsewhere in town illegally parked bikes would be removed on short notice and auctioned if nobody reclaimed them.

In Tokyo I did not dare to venture out on a bike when sharing an apartment with two Korean blokes. One of them had a bad accident once and that scared me away. This was in the western suburbs, in central areas where the streets are more linear it might actually be doable better.