The country location for a company in this research was determined by where the bulk of the employees are currently. The intent of this definition is to show which countries are most capable of building big internet companies, not where the founders are coming from.
Yahoo!Japan is actually an independent company from Yahoo. It is roughly 30% owned by Softbank and 30% owned by Yahoo. It is listed as it is the top 3 internet company in Japan.
Yahoo is not listed, because it is not the top 3 company in the US.
But then again, it lists Yahoo! Japan as Japan's first. And I feel that while Yahoo! Japan probably was founded in Japan, Yahoo! sure wasn't.