I'm not a Japanese but I have a different take on this.

I believe that this is largely because both the decision makers and the target consumers are relatively older in age. They are very practical kind and can't appreciate the concept of modern design.

The decision makers would hope that all the informations you need could be found in a glance, just like the layout of a newspaper. And they want everything to 'pop', in a way that it should steal your eyeball right away, not realising that if everything 'pops', then nothing actually pops.

On the other hand, most consumers that actually spend money are not young either. Not seeing a busy website (especially marketplace) gives them a feeling that the website is abandoned and not updated, so it's easy to see a trend which, the more it pops, the better it sells.

As you have mentioned, it's a web-design specific problem. Japanese are actually very respective of spacings in graphic design, and they're the leader at it.

I believe this busy trend is slowly fading away, though. It has already gotten a bit better in both Taiwan and China recently (in Japan too I believe, such as Muji and Uniqlo), as the previously-younger generation has grown older and thereby emerging as the new main consumers.