Most US software companies with on-the-ground operations in Japan will want to have Japanese subsidiaries. You'll want to have Japan-based employees. This obligates you to pay Japanese employment taxes, contribute to the Japanese retirement system, and arrange for Japanese healthcare. Having a Japanese subsidiary is one of those things which I suspect is not an actual requirement but which your competent legal counsel will say will save you hundreds of hours of explaining yourself at the local ward office.
Additionally, after you have a subsidiary, you have a very straightforward way (intra-company transfer) to get e.g. US employees work-capable Japanese visas in a fashion which is very not straightforward if you lack a Japanese entity. (If you have e.g. an engineer who you want to place in Tokyo who doesn't come with e.g. Japanese citizenship, permanent residence, or a spousal/parent visa, then getting them an engineering visa requires roughly three bullet points, one of which is a contract with a Japanese organization to do engineering work. It's a black letter law requirement and you will not be successful in getting an engineering status of residence without it.)
n.b. Not a lawyer, not an accountant, but if anyone from the US is ever getting an office set up here drop me a line and I'll give you the quick rundown.
Probably for support / sales / community outreach based stuff.
Lots of people in Japan, even techies, have less than stellar English skills. There are also a lot of companies here that are still in the dark-ages when it comes to technology (e.g. I worked at a company that tried CVS in 2009 before I joined but didn't see the point of version control)
Sales / Support staff fluent in Japanese will help a lot I think.
Japan has 130 million people. I think there is probably lots of room for Expansion for github. Having a Japanese sub also makes taking payments easier, I am sure there are other legal / administrative reasons.
Like theyeti, I worked in a company that wanted to do business in Japan - they wanted to buy some advertising there to get the Japanese audience - and advertising companies refused to work with them (to take their money that is) because they didn't have an office in Japan. That is when you want to buy something from Japanese companies, I can't imagine how hard it would be to sell to them without an office there.
