Sexual crimes are massively under reported because of conformity culture in Japan. Even there has been a massive problem of groping and upskirting women in public transport to the point Japan made new laws to tackle this, so it's not like sex crimes are super rare there.
The other issue is that pretty much anything short of actual violent rape is considered, effectively, a civil matter to be settled by the parties with a cash payment.
Slide your hand up a middle-schoolers skirt? Pay 20,000 yen and have your lawyer convey an apology for the "misunderstanding". Suck some underage penis? This 15,000 yen and a most humble appology for grooming your 5 year old son.
There are plenty of cases of adults having sex with minors or molesting kids in Japan, they just don't get caught. Japanese prosecutors don't pursue crimes unless it's an open-and-shut case (hence the "99% conviction rate"). These sorts of cases always have tons of hearsay involved and their culture pressures the kids to not speak about it because it's shameful for them. I have no doubt Japan has just as many pedos as anywhere, if not more. I mean, many people there don't see anything wrong with a 14 year old middle school student dating a 30 year old teacher (including the students).
You touch on two other issues:
1) Victim Anonymity laws are very weak in Japan. If you testify its expected your identity will be known even if its not in the official record. Teachers will know, your school mates will hear the rumor. The government will sometimes offer, essentially, relocation and name chance, but that means rebooting your entire life.
Basically, victims will feel pressure if not directly from their families from society to handle everything non-judicially, quietly, behind closed doors.
2) In a shame-based society, if the DA fails to secure a conviction it is a huge blow to the honor of the person "falsely accused". So in a lot of cases of sexual crimes they will say it heresay and basically use their political weight to force a settlement payment from the molester and get them agree to a restraining order. This is viewed as a good thing because the victim doesn't need to go through a court trial or otherwise have their shame and defilement, that they are "dirtied", made public.
When I visited a friend in Japan, there was some marine rape case that was in the news at the time. One of the Japanese guys told a fairly fucked up story where there was a known boyraper in town but all of it was handled outside the courts. All the local parents knew to warn their kids to stay away from that area of town, he'd been pressured to move to some run down place near the local factory, and the factory workers would remove anything he put out to bait in children, like swings or whatever, and in general keep an eye on activity. Basically rolling in a dozen deep to on the regular make sure the boy fucker understood what would happen if touched any of their kids.
Anyway, while all the locals knew to make sure their children avoided Touchyfeery-san's place, but when families moved in word was very slow in getting to them. He said one of his new classmates who moved in part of the way through elementary got his bootyhole snatched; he didn't know that at the time, just the kid disappeared from school and later on when he was more aware of what had transpired asked his parents about why the new family wasn't warned, his mother said something to the effect of "She (Boy's mother) never really fit in with us (the town moms' group)".
I think about that when people talk about how great and crime-free Japan is.
