I think it has to do with the Yakuza: when a member of this organisation will leave it, they have to chop of one of their fingers. Everyone in Japan will discriminated who hasn't 10 fingers - they fear to be associated with the Yakuza. So many people, who have lost a finger in an accident or thanks to the japanese Mafia, wear protheses. Same discrimination-problems do you have, if you're tattooed. It also shows your membership.
Some tourists got problems about that, when they went to public baths, ect. But back to the fingers.
It's a problem, that affected also other characters from other parts of the world. Mickey Mouse for example has 5 fingers in Japan. Diddy Kong was created by Rare in Great Britan and I guess they don't know about this problem first, but after learning about it, they may have corrected their mistake.
€dit: it also came to my mind, that 4 is called "shi" in japanese, what could also mean "death". So the japanese try to avoid the 4 like the most americans and europeans do it with the 13:
There is no 4th row in planes, no room with the number 4 in hotels, eventually a building misses the 4th floor, ect. Also, if there is a fictional character, who should be drawn simpler, japanese will tend to took two toes instead of one. Chip from Sonic Unleashed is a example for this: