According to the Japan Times, Tokyo’s very first night bus has started running once an hour from Roppongi to Shibuya and back. Reasons given against underground trains doing the same in the article include the need for maintenance (something other places somehow get around) and salarymen not wanting a reason to work even later (i.e. not to lose the excuse to leave of the last train home).
What the article doesn’t mention is the ability of well organised and pushy taxi drivers to block proposals like this – including in some countries their apparent ability to make sure that there are no other easy ways of getting to the airport! Given the famous electoral influence of farmers and owners of small shops in Japan, I’d be very surprised if taxi drivers don’t also have a real impact on policy.