I'm surprised this article got so many upvotes. It's a lot of anecdotal evidence, and even the anecdotes and websites they pointed out don't support the point that much. http://yahoo.com and http://yahoo.co.jp both have similar, tight aesthetic with a lot going on. http://youtube.com (view in incognito if you are signed into an account http://nicovideo.jp are very similarly information-dense. I'd say Youtube's layout…
About a year ago, yahoo.com and yahoo.co.jp looked rather different. Yahoo! Japan's portal was astonishingly cluttered. Then it seems that Yahoo! HQ cracked the whip and ordered everyone to get in line, so the Japanese site became more like the US one. Still pretty messy, but nowhere near the sensory overload levels it reached before.
Now, it looks like Yahoo! have cleaned up their site more, and turned it more into more of a "What's hot!" portal. But, on my browser, Yahoo! Japan hasn't changed yet.
Of course, the article is cherry-picking a bit, but I don't think it's being unfair. Popular Japanese sites, including big e-shops, are garish and cluttered to a degree that would be unacceptable in the West.