Actually, the demonstrations are usually held by right wing Japanese organizations on August 9th, the day of the bombing of Nagasaki.

This was also the day that the Soviet Union broke the neutrality pact with Imperialist Japan and invaded Manchuria and other parts of the Japanese Empire. The protests are usually against this invasion and consist of calls to get the Northern Territories of Japan returned.

Also, there are angry tantrums and shouting, but there are no throwing of empty bottles at the walls of the embassy because the riot police do quite an impressive job not letting any of the protestors through. It's a bit of a charade and an annoyance when you're trying to conduct business in the area, but the reality is different from the story you're sharing.