I don't believe the US had any more nukes after the first two were deployed for at least another 6 months.
I think we figured the necessity for more would be a non issue after the japs saw what we did to their cities.
There were 6 made, one Uranium (which was low risk of working) one plutonium was tested at Trinity. (the US dropped the first nuclear weapon on its own soil!)
The Indianapolis brought 4 bombs over less the cores. 2 were brought by air.
All the cores were brought by air, and the third core arrived about the same time that Bock's Car returned from Nagasaki.
The Japanese physicists analyzed soil samples from Hiroshima, and advised the Japanese government that it was a bad miracle, a one time catastrophe, based on the difficulty of separating U235 from U238.
The same team of physicists found Plutonium reaction products in soil samples from Nagasaki. They knew that plutonium could be chemically separated from Uranium, and that there was no limit to the number of bombs that could be made.
Also the Japanese 14th army group had been overrun by the Soviets. They had counted on that army to prevent use of Chinese manpower against the home islands. No only was that hope gone, but the resources of the Soviet Union were now arrayed against them from the north, taking Saklin Island from the north.
The Japanese strategy at that time assumed that if they took 30 million casualties, they could force the US to negotiate. Based on the 30-1 exchange rate on Okinawa, they were sure that the US would not accept a million more casuaties. The combination of nuclear weapons (any defensive line would be immediately broken) and the larger manpower reserves of the Soviet Union, added to China and the US, meant that strategy had failed.
We knew all this because of US proficiency in reading the Japanese diplomatic codes. (MAGIC)