That's one thing I thought was a little disappointing when I was in Tokyo. The trains stop at midnight on the weekends, when I would miss it I'd have to stay out till they started up again. In Germany, at least in bigger cities, they have on weekends and holidays that public transit goes all night.
Then, why encourage people to stay out late...
In northern Europe you often hear the safety argument for affordable night-time public transport - “without that people may catch a unlicensed cab or try to walk home and get robbed, or worse”. But in Tokyo you the risk of something happening to you even if you pass out on the sidewalk is very very low.