There are many theories as to why many Japanese websites are cluttered. Most revolve around some cultural notions of how information is processed and space is commoditized. However, it can also be attributed to the process behind how most sites are built than any cultural preference.
Websites, or rather those that commission them, often find themselves stuck between the softer marketing and advertising approaches and the harsh technical utilitarian approach of developers and engineers. The engineers have been winning this battle for years in part because they win the technical debates. But slowly, economics and mobile devices are changing how website are perceived and used. And this is a good thing for those who find websites in Japan confusing.