This is a genuine question. There's probably an explanation for this I haven't thought of, but it just occurred to me and I thought I'd post it here. I'm sure a central reason would be that Japan was going to surrender, while Germany wasn't at the time.
the bombing of nazi germany was a war crime, as was the firebombing of japan. sometimes you gotta do war crimes to make an enemy to concede defeat, and there's no tactic that shouldn't be used, if necessary, to defeat fascism.
atomic bombs were completely unnecessary though, and they were used to scare the ussr not to make japan capitulate.