Concerning the topic "nuclear bombs and low popularity in Japan": Basically, I agree. I can only shake my head when I see the millionth US-american movie or game in which the Nazis play the role of some aggressive clowns. Then again, I don't have a problem with such things appearing in CIV, not even with the usual "fascist patches" or "Hitler leaders". History is a mix of good and evil - it would be unrealistic to hide the ugly parts.
However, i definitely kan understand IkimashoZ. We don't have KZs in our games, either, and for the better. I noticed, too, that in CIV4 the moral lesson of earlier versions seems to have eradicated and all the other civs do NOT declare war after you dropped the bomb. Together with the non-existent pollution, I see this as one of the big drawbacks of CIV4, game-wise. In earlier version, it was a game you could give to children and they could learn a lesson from it. This aspect has decreased considerably, sadly so.