Hiroshima and Nagasaki were not uniquely un-bombed. (Nagasaki was, in fact, bombed in small ways, including just days before the atomic bombings, because it was never put on the "reserve" list that Hiroshima, Kokura, Niigata, and Kyoto were, contrary to many incorrect sources.) There were many mid-sized cities in Japan that were not yet significantly attacked as of early August 1945. So it is not quite as obvious at the time, as it would be in hindsight, that at least Hiroshima was being "reserved" for something else.

That being said, there are post-bombing accounts from people in the city of Hiroshima where they said, in essence, we saw so many cities around us getting bombed and we figured it would happen to us any day now. Of course, there is a risk of confirmation bias in such a thing. But they were certainly aware that there were many cities nearby under attack (notably Kure, which was just next door and was attacked many times during the war) and aware that they could easily be among them.

I have never seen anything that suggests the Japanese high command were looking at any list of as-yet-unbombed cities and wondering about them. If they did, it is clear they would not have been thinking about atomic bombs — they were not at all concerned about those being used prior to their actual use.