I think it's because a website isn't a "downtown." It's more like a single building rather than an environment built by thousands of different people. But where is the Toyo Ito of Japanese website designers?
It's true those may be reasons why they look like they do, or part of the reason, but I think it's a question that is interesting. Even if Japanese websites get their "language" from those things, it at least seems like they should get their language from other places also, such as modern architecture or industrial design.
> such as modern architecture or industrial design.
Except for some landmarks, temples and gardens, contemporary architecture in Japan is surprisingly ugly and noisy.
I think most of the big sinners of Japanese webdesign are stores (at least the examples I can think of) and something like Bic Camera is more noisy and flashy in real life than their web presence.