There used to be a very seedy old hotel at the SouthWest corner of 6th St. and Mission St. when I last lived in SF in 1999. It seemed to be full of displaced people at the time.
There was another hotel I actually stayed for New Year’s 2000 that was very close to the entrance to Japan Town (can’t quite remember where that is) and about 85% of it was residential, and the rest for nightly guests. It had a sort of rundown shabby chic and there were a lot of “characters” who had lived there for ages.