I am far from being a person who has deeply studied Japanese culture (I just happen to live here) but my impression is that it is so ingrained in the mentality that it works at a subconscious level.
In my own limited exposure, most designers I have encountered worked by feel and experience instead of analytical principles. I've definitely heard people say that a part of the page feels a bit empty or get some evaluation to that effect from peers. It's much rarer to hear someone say something looks too busy or crowded.
I suspect that in the long grind to "polish your work", there's a simply tendency to remove all these "empty feeling" spots more than to "trim the fat".
This reduced the problem to why there's a bias for things to feel empty instead of busy. To venture a bit of personal sociology here, my experience makes me feel like Japan produces a bias toward more intentional and deliberate behavior. Or worded less charitably, we could maybe call it fussy?
Accepting this idea, in web design we'd expect a bias toward needing deliberate explanations for every aspect of the page layout, including every bit of white space that someone might point out.
I think it's interesting that "Japanese design" in almost every other area hints at a certain functional minimalism, that stands in stark contrast to these sites. I mean sites like, ironically enough, the Css Zen Garden (http://www.csszengarden.com/), highlight the western perception of their design principles: lots of white space, consistent design, minimalism.
White space is luxury for the eyes.
That makes that, when they present a design, it has to look like they worked really hard in the design. That's why there is always so much information.
To the eyes of an executive who has no idea of design (most of them) a minimalist design would look like if the designer was lazy and didn't work hard enough.
Of course, I am exaggerating.... But not a lot.
Source: Working as a Web Developer in Japanese companies in Japan since 5 years ago.