Yes, the candalism of Anne Franks books in Tokyo says something about Japan's society, because the books were about World War II. Their vandalism shows that there are still some residual opinions of hate that led to the violence of World War II. It is a good thing that we still have a presence in Japan.
As Anne Frank was a victim of one of the most appalling tragedies of mankind to vandalise books representing her is like spitting in the face of all of the holocaust victims. The vandal more than likely knew what the book stood for also. It does show that in Japan there are some anti-Semitic, and perhaps extreme political view, most likely fascism, present in Japanese society. But Japan alone can not be held accountable for this vandalism.
I think the important thing to look at here is that they destroyed books. Generally most people in the west see books, especially historical ones, as being significant socially. If you look back, Germany also burned many books during world war II and most people see that as being bad, along with Nazi Germany.
I don't think that the actions of a few individuals can have that sort of impact. Like others have said. A couple terrorists can't represent all Muslims. If you think that a few individuals could represent Japan's society. That's 128 million people. Then I think you're pretty darn close minded.
Every culture has weird things arise like this. The Japanese a very well respected people with an outstanding culture. This does not by any means say anything about the society when there is no proof that all or even the majority of people are doing this very terrible act of vandalism.
Just as a couple terrorists do not represent the entire Muslim community, and as the KKK does not mirror all American white people as a whole, a group of vandalizing bad apples cannot possibly be used to stereotype the entire 128 million people nation that is Japan. It's just ludicrous.
It is my opinion that the vandalism of Anne Frank books is not a commentary on Japanese society as a whole. There are many acts of vandalism that take place in every nation by various groups of people, but if the entire society is not taking place in these acts, than any social stigma that is attached to the vandals should not be attached to the society to which they belong.
Japan should not be held accountable for the actions of a tiny minority of it's citizens. Just as Muslims should not be indicted as a whole for the crimes of a few. And just as whites should not be stereotyped as skinhead racist rednecks. These people who burnt the books should be treated as individuals.