Keep in mind, the availability of nuclear weapons was unknown until they came into use. Also, it was unknown how effective they would prove in practice. The plan of record was to invade the Japanese home islands, using carpet bombing and chemical weapons to gain as much advantage as possible.
Also, the production of atomic bombs was constrained to around 3 or so bombs per month by late 1945. Which is significant but would have been only comparable (rather than greatly superior) to the destructive power of the conventional strategic bombing campaign. Even without atomic bombs Japan would have been utterly devastated by the end of 1945 had the war continued (every city destroyed, most of its shipping destroyed, most civilians starving and/or homeless).