Curfew - Is walking on the street in Tokyo legal after 11.00 pm if you're under 18?

The relevant legislation is here (in Japanese). This is only for Tokyo, the legislation in all other prefectures is similar but may differ in some details.

Basically, it's "illegal" for parents to allow a minor to go out between 11pm and 4am except for going to work/school or for some other "justifiable reason". What constitutes a "justifiable reason" is as usual unspecified and left to the judgement of police officers/judges/etc. I put "illegal" between quotes because the ordinance says you must not do it but it's not clear what the penalty is, if any. It's also not clear if hotels are considered "home", so it's possible that he will technically be out of his home anyway.

Edited to add : there is a difference in interpretation between jpatokal and I, so here is mine in more detail. jpatokal correctly translates clause 1 as saying that a parent must not allow a minor out between 11pm and 4am without a "good reason". However, in his commentary below his translation, he adds "by themselves". As far as I understand the Japanese text, there is no reason to add this, and clause 1 applies equally no matter by whom, if anybody, the minor is accompanied.

Clause 2 forbids anybody from accompanying a minor out without a "good reason" or parental consent. Presumably, the bar for a "good reason" is higher here, since it allows anyone to take a minor out without parental consent, maybe even despite parental oposition in extreme cases. In normal situations, however, parental consent is required, and by giving it without a good reason, parents violate clause 1.

Other edit : I will also add that the bar for a "good reason" in clause 1 is probably quite low. Yesterday at about 11:30 just after first posting this answer, I went to the convenience store to grab some late night snacks. There was a boy probably no older than 10 with his father also buying stuff, and the staff didn't say anything. So being hungry and needing to buy food probably qualifies. (I am not in TOkyo, but the law where I live is similar.)

In reality, as long as the boy is accompanied by an adult, just walking on public streets in Japan late at night won't cause a substantial problem in most cases. If you are unlucky, a police officer might stop you and ask a few questions, but anything worse is unlikely to happen. Entering certain safe stores like convenience stores is OK, too.

But I don't recommend taking your child out to certain red-light districts like Roppongi or Shinjuku. It can be a risky thing, both physically and legally. I'm not really good at legal talks, but according to this Japanese lawyer, I think the interpretation by @fkraiem is correct:

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(My translation: Even when accompanied by a guardian, for example, if you took a youth to a nightlife/red-light district, that would be a subject to confines. Accompaniment of the guardians does not mean everything is allowed.)

If you violate this legislation in question, theoretically, you might be fined up to 300,000 yen. (Because your son is under 16. Oddly, there is a written penalty regarding youths under 16 (not 18). See ?26??5?.) But I guess the worst thing that can actually happen in your case is that the police officer tells you to return to your hotel with your son immediately.

And many kinds of shops and facilities deny admission of people under 18 after 11 PM, even when accompanied by an adult. That's a regulation imposed on the shop's side. Such shops/facilities include restaurants serving alcohols (aka izakaya), movie theaters, karaoke boxes, amusement arcades.