...attend school an hour later than normal, at 10am...
My entire high school started at 7:30 a.m. every morning!
These kids had it better than most already.
Based only on the article description, Japanese citizens are being assigned ID numbers, not ID cards. Using an ID card to authenticate yourself works well because it probably has a photo and maybe a fingerprint on it, as well as some other personal information. If someone uses your ID card, it's easy to catch them. On the other hand, using an ID number alone to authenticate yourself is a terrible idea because it's a lot easier to match an ID number with a person than using their ID card. The ID number is treated as a kind of password, as if only you could possibly know your own ID number, despite the fact that you give it to anyone who wants to know who you are (which they assume also proves that you're you). The odds are high that eventually someone, maybe even you, will make a mistake and someone else can then tie you to your ID number.
What's funny is that the U.S. government discourages you from using someone's social security number to both identify them and authenticate them, because of the obvious security problems we see every day. Yet businesses continue to use those numbers for authentication. An easy fix would be for the government to simply publish everyone's SSN at once. Then any business that uses SSNs to authenticate people will be castigated or lose business for being idiots.
I think it would be cool to separate authentication from identification. Everyone gets a unique ID number and chooses a private code that together produce a public code, or maybe many one-time throw-away codes, that you can use to identify yourself without giving away control of your identity.