I don't think the motivations were unclear at all: They were in a Total War where there was no distinction between military and civilian targets, and they had a new, powerful weapon; of course they were gonna use it. There was never a discussion as to whether use it or not. The immediate political effects of the bombs, if they were really the main factor in Japan's decision to surrender for instance, are indeed murky, though it was most probably Soviets entering the war that did it more than the bombs.