As always, take Japanese crime statistics with a large grain of salt. I remember the Japanese police have quoted something like a 90%+ clearance rate (uh, yeah, right).

Also, do I remember incorrectly or did they not go on a serious campaign to break the yakuza at the same time?

A lot of petty crime is enabled by the organized crime providing the infrastructure (fencing, financing, etc.) required for individuals to be able to convert their crime into money.

(See, for example, the current "shoplifting" spree in the US or "bike theft" rings. While individuals often commit the crimes, gangs are the big enablers by functioning as fences. It's why your stolen bike can wind up in Mexico before 24 hours have passed.)