Speaking as a Japanese-American, I personally think the biggest problem with Japanese programmers comes down to the Japanese being too crafty and elitist.
What do I mean by this? Basically: If you're a wizard at peeling the skin off an apple with your knife you never need an apple peeler; consequently, you never get a good peeler industry going. Meanwhile, Americans manufacture the best apple peelers because they can't skin an apple with a knife to save their own lives.
Likewise, Japan doesn't /need/ or /want/ the conveniences and luxuries afforded by genuinely good programming. Japanese can and will get by with the hard(er) way and won't care.
Tools exist to address an inconvenience. Good tools exist to make a convenient inconvenience even more convenient. And good toolmakers exist to enable such better conveniences. None of this can exist if there aren't inconveniences in the first place.
This also extends to the hardware side of things, too. Take flash memory, for example. Flash memory was invented in Japan by Toshiba, but nobody cared because Japan was too good. Meanwhile, Intel and the west seized upon the invention and made bank.[1] We all know where Toshiba is now.
This I feel is why Japanese programmers continue to be utterly inept (most still can't produce unicode programs), and why the wider industry in Japan continues to be irrelevant on the world stage from a programming perspective. There is no Japanese equivalent to Microsoft or Google or Amazon because Japan's too good for that.
[1]: https://en.wikipedia.org/wiki/Fujio_Masuoka