I think they're comparing apples to oranges.

If you're looking at Rakuten then compare it to Amazon and eBay which are also pretty cluttered but functional.

If you're looking at Yomiuri then compare it to New York Times or CNN or Fox News all of which are pretty cluttered but functional.

That minimalist "clean" look isn't a general trend of e-commerce and news sites even in the US, if that is what they are using as a reference point.

Japan has no shortage of modern web design either. You just have to be looking in the right places, e.g.

This temple https://www.kiyomizudera.or.jp/

This Michelin restaurant http://akiyamashirokane.com/

Mazda https://www.mazda.co.jp/

This tea house https://www.fukuda-chaya.jp/

This startup https://www.kudan.io/jp/

This web design dude https://kuon.space/

This startup accelerator https://www.j-startup.go.jp/

This website about traditional Japanese colors https://nipponcolors.com/