It could be because it's very humid which tends to heighten bad odors or cultural development but, the Japanese can't stand the bad smell and dirty things. For example, when girls were asked which they prefer - a handsome guy with bad hygiene or an ugly guy with good hygiene, they all picked good hygiene. When Japanese mop the floors, they finish with wiping the floor with a rag to clean up any residue mop water - in the west they let the dirty film of water dry out; gross, I will never lie down on a western floor.
People bath every day and before and after s*x - before to make themselves presentable to their partners and after to clean themselves of varies bodily fluids( tissue paper is on stand by during s*x to wipe off "stuff" after the act lol). Other clean aspects of the bathroom are people wear special slippers when entering the bathroom, every home has a washlet and Japanese shower before they take a hot bath. Sensitivity to smell is also the reason Garlic and coriander never got popular in Japan.
Also a difference to the western world, Japanese Idea of clean means "organized and not soiled" but does not mean "matching or worn". Often a Japanese home is a hodgepodge of mismatching furniture with neat stacks of magazines conveniently placed around the living room, it's never a showroom, it always looks lived in. Also, on public buildings the railings and metal poles will show a lot of rusting yet no one seems to care, no one thinks of this as dirty. At home, the stove and burners in Japanese kitchens often show blackness in the hard to reach areas. Japanese never clean their stoves speck and span like they do in the west. surface cleanness in Japan is about hygienic so scrubbing for hours or using toxic chemicals to remove the dark polymerized oil stain is pointless. As long as it's clean and free of germs then it's good, no need to be stain free in the kitchen.
Yet leave things out or disorganized or unhygienic and everyone will say "Kitanai!" - "So Dirty"!