The best study that I am aware of was by Geert Hofstede on cross-cultural analysis, where he compared individual cultures and perceptions across thousands of professionals around the world. The result was that there were clear cultural differences between countries. But the most interesting thing was that the differences within countries were greater than the differences between countries.
I would expect there to be cultural issues in design (like red or white having different meanings), but the fundamental principles aren't culturally based. Good UX is based primarily on cognitive psychology and perception - which varies very little across cultures.
For the record, I have done some UX testing that included two Japanese women, and the results from them were no different from the results from the rest of the group. So although this is a small sample set, it adds weight to the idea that in its fundamentals, UX shouldn't change across cultures.
As a small experiment, I would suggest doing some ninja UX testing on two sites. One with a typical design that you are being asked to create, and one with good UX principles. Then come back and update your question with the results.
As an aside, Japanese culture is very traditional (high uncertainty avoidance) and one where you shouldn't question your boss. Given that designs that you have shown seem to be taken from the earlier days of the web, I would hazard a guess that people the designs haven't changed as much because people have kept to tradition and not challenged the way that their boss says it should be done.