Well i can't speak for all of japan.
But tokyo is a very clean city they have a clean attitude on things. Probably due to their continuous on the go feeling.
And also isn't japanese tradition to clean your hands and such before every meal for a example
in america your mom always tried to get you to do that but it comes and goes as you get older like whatever.

As for cigarette smoke damage and smells

In Tokyo your older generations chain smoke like its going out of style (mostly your low income individuals) one after another after another after another.
once you get outside tokyo to your more rural japan areas smoking is kinda a norm... helps the farmers relax i guess.