Sex crimes in general go underreported, not just in Japan, but everywhere. Japan also has been working to making more acceptable for victims of CSA and rape to come out about their trauma. The main reason that sex crime rates are as low as they are is not because people are afraid to come out about, it’s because of cultural taboos.
In Japan, it’s less acceptable to have outbursts of aggression and passion (and sex crimes do have that to some extant), not to mention the fact that the crime is already low. It’s a common practice to add 20% to sex crime statistics, especially when accommodating for the “dark areas”.
Even without 20% and the underreported crimes, the CSA and rape rate would still be low in Japan.
TL;DR: Sex crimes are under reported everywhere, not just in Japan, Japan is making more acceptable for victims to come out about, emotional outbursts are a no no, crime in general is low, 20% is added in dark areas, rape is is low even without the 20%.