The Japanese have the perfect answer. They don't zone by use. They zone by nuisance level.

You can build whatever you want in the cement-plant-district. But you have to deal with having that kind of nuisance nearby. You can also build whatever you want in the no-nuisance district. But you can't impose any kind of nuisnace.

Do you have a source for that? According to this article[1] which is summarizing an official Japanese zoning document [2] they have 12 well-defined zones.

They're overall more relaxed about mixed-use zoning, but they do have exclusively industrial zones, and exclusively residential (with small shops & schools) zones.

1. http://urbankchoze.blogspot.nl/2014/04/japanese-zoning.html

2. http://www.mlit.go.jp/common/000234477.pdf

How do they deal with the tension of having bars/clubs in residential areas? Or do these areas just not exist in Japan?

We happily walk to the bar from our houses and then walk back after having a few drinks.

One of the advantages of having bars in residential areas is that you don't concentrate them in one area. Unless you live in a big metropolis, the bars are not large, are not noisy and don't cause many problems. To be fair, I don't know how dance clubs are zoned. I have never seen one outside of a reasonably sized city. But, you can definitely hear people croning away in the karaoke clubs at night.

Probably the same way SF deals with it: by not dealing with it because it's not an issue. I lived in an apartment building on the same block as at least one club and multiple bars, all open till at least 2am and it was never a problem. Some of the sound will leak into the street, especially with bigger clubs, but it's not loud enough to be a problem inside apartments because air is a terrible conductor of sound. Also, a city is already noisy and that's to be expected 24/7.

I live in a "small" Japanese city (pop 300,000). I've only seen clubs in the central entertainment district. There are lots of small neighborhood pubs interspersed among houses though, but they don't cause any nuisance.

If you want silence at home, move to the country. The notion that urban spaces should be free of human voices at any hour is ludicrous. No loud music after midnight is reasonable, but other than that if you can't sleep install better insulation. No one is forcing you to live in the city.