It was weather that made the targets hard to locate.
Weather did impact thefinal choice of one of the cities, but there wasn’t much left of most major industrial cities of any consequence.
http://apjjf.org/-Mark-Selden/2414/article.html
“Overall, bombing strikes destroyed 40 percent of the 66 Japanese cities targeted, with total tonnage dropped on Japan increasing from 13,800 tons in March to 42,700 tons in July. [31] ...
Overall, by one calculation, the US firebombing campaign destroyed 180 square miles of 67 cities, killed more than 300,000 people and injured an additional 400,000, figures that exclude the atomic bombing of Hiroshima and Nagasaki. [32]
Between January and July 1945, the US firebombed and destroyed all but five Japanese cities, deliberately sparing Kyoto, the ancient imperial capital, and four others. The extent of the destruction was impressive ranging from 50 to 60% of the urban area destroyed in cities including Kobe, Yokohama and Tokyo, to 60 to 88% in seventeen cities, to 98.6% in the case of Toyama. [33] In the end, the Atomic Bomb Selection Committee chose Hiroshima, Kokura, Niigata, and Nagasaki as the pristine targets to display the awesome power of the atomic bomb to Japan and the world in the event that would both bring to a spectacular end the costliest war in human history and send a powerful message to the Soviet Union”