First Japanese are not especially clean, we might get that impression because they often wear mask and seem to fear germs that give them an image of being mysophobia, but the couples of times I have to Japanese home, I could not help but notice the amount of dust on things or grease in the kitchen, also hoarding is quite common either in a room, on a balcony or around the house.
But I would say generally they take one shower or bath once a day, never seen people that were taking multiple shower or bath per day, usually bath before bed, unless if you go to the onsen or if are especially dirty for some reason. (I think this is a bit the same as for other countries)