I think this issue is a class thing. Book shoplifting = lower class. Jail is fine for them -- at least if repeat offenders -- even though most books at Barnes and Noble are destined to be pulped, so stealing them deprives no one of anything. By contrast, book piracy = upper middle class. So punishing them is a horror, and, unlike with every other kind of stealing, conviction should require a showing of harm.
This is not to defend the Japanese law, which I do consider draconian. It's so draconian that I doubt it will be enforced. Cutting off internet access would make the punishment fit the crime.