I think there are two things here: first is that Japan is so safe that police is actively looking for cases to pursue. I remember reading of police putting (as a trap) a case of beer in an open car at a shopping plaza, monitoring it for a week before finally nabbing a retiree who opened a door (whether to "steal" the beer or just to investigate). In and of itself such safely is, IMO, something to celebrate. The secon…
The 99% figure is a common misconception. Prosecutors in Japan are underfunded, so they only try to convict rock solid cases, among other factors. This Wikipedia entry seems to flagrantly defy wiki rules but seems more informative for it. https://en.m.wikipedia.org/wiki/Criminal_justice_system_of_J...
Because suspects are put through continuous interrogation which could last up to 23 days as well as isolation from the outside world, including access to lawyers, both the Japanese judiciary and the public are well aware that confession of guilt can easily be forced.