I have no sympathy for Fischer, whose public statements seem anti-semitic and generally offensive: "making strong attacks on what he called "world Jewry", and calling the 2001 terrorist attacks on the US "wonderful news"" according to a BBC article.
But I think that Japan is being inconsistent in who it chooses to extradite. Peru has been seeking the extradition of ex-president Alberto Fujimori, who "is wanted by Peruvian authorities on nearly 20 charges ranging from corruption to allegedly authorizing a counterterrorism death squad" (according to another BBC article) but:
The ex-president has been living in Tokyo, protected from extradition by citizenship extended because of his Japanese-born parents.
Fujimori was not born in Japan and has never lived there, in contrast to Bobby Fischer who has spent the last three years as a resident of Tokyo. In a just world, any special duties of a government should be to residents as well as citizens, and citizenship criteria need to be fair, not based on racist ideas. The current Japanese laws on citizenship count in "ethnic" Japanese abroad, and rule out children born in Japan to Koreans and other 'foreigners'.