There were 63 civilian casualties, mostly from AA shells falling on Honolulu. The Japanese were mainly flying over military installations, but any vehicle moving near an airfield or the harbor would have been considered fair game for them, and it wouldn't be a surprise to me if they took shots at what they would have seen as "targets of opportunity". Given the relatively low numbers of civilian deaths, again mostly from friendly fire, it's doubtful that the IJN pilots went out on a shooting spree.
Also, any building actually on an air force base would probably have been shot up as well, even if it was civilian housing.
The incident of the Japanese pilot trying to shoo the kids on the baseball diamond away from the fight actually happened.