The Japanese do indeed have a long and highly cultured history.
Their history is also replete with examples, practiced on their own people, of the kind of barbarity they exhibited on other peoples in WWII.
IOW, being cultured will not prevent a nation from committing atrocities. The Germans, as an obvious example, were perhaps the most highly cultured people in the world in the 1930s.
If you had gone around in 1912 telling people that in 30 years the Germans would be shoveling people into incinerators by the trainload, you would have gotten a life sentence in an insane asylum.