Employees at Japanese companies typically don't speak English (this includes engineers), so they're hesitant to hire someone who may cause communication/cultural problems.
They also generally don't have the same attitude towards hiring and are definitely not hiring for top talent. People are hired because they fit in the company culture first, and because they have potential second. Young engineers are paid cheaply and are not expected to be skilled; they are trained on the job.
Somewhat related: http://news.ycombinator.com/item?id=3845850
It's definitely possible to get hired as a foreigner in a Japanese company, but it's not easy and the conditions are not great, compared to Facebook et al.
I didn't know they accept non native engineers; that's another thing I forgot about; if a company really would like top talent, what's with the closed-border mentality? If Facebook doesn't have that, then kudos to them. If you want talent, it shouldn't matter where someone is from right?