I think that long distance local trains on "long distance lines" (e.g. Tokaido main line, Takasaki line, Joban line, Tohoku line) typically have toilets. Commuter trains and shorter lines don't. (How long must a line be to qualify as a long distance line? Your guess is as good as mine. How do you know if your train is a commuter train or a long-distance train ... It might take some detective work to find out).

You can check the rolling stock used on each line through Wikipedia. For example, Takasaki Line is moving to E233 Series stock. Wikipedia describes the layouts / disabled access / toilets:
https://en.wikipedia.org/wiki/Takasa...#Rolling_stock
https://en.wikipedia.org/wiki/E233_s...33-3000_series

I think the big, printed, timetables might have icons to indicate whether trains have toilets on board. I haven't looked at one of those for years.

Train toilets are way better than I remember them from 30 years ago. Using a very smelly washiki benjo on a shaky train was like a rite of initiation to test a young Japanophile. I think those stinky WCs were converted from "hole in the floor" toilets that dropped waste onto the tracks. The facilities on modern Japanese trains smell much fresher.