Not too long ago two anime were released that were both set in the early postwar period --
Mouryou no Hako and
Nijuu Mensou no Musume. Even though they come from very different genres and target rather different audiences, they both included material on human experimentation and war crimes. I guess the fact that World War II is so far removed from the contemporary anime audience has made it possible to consider Japan's actions in the War however obliquely.
Senkou no Night Raid is set in prewar Shanghai and purports to tell the story of a secret spy agency being used by the Japanese in China. Unfortunately for me the fact that the members of the spy ring all had superpowers made it much less compelling than it might have been.