They worried a lot about missing the target. People think of the atomic bomb as some kind of all-powerful city destroyer, which it can be, but its range of effect is only a few miles. So if you are a mile or two off, you will have wasted a billion dollars with little to show for it. And the scientists and military who were in charge of making the bomb worried very much that it might be "misunderstood" if its first use was not spectacular. ("Misunderstood" both by the Japanese — who might not perceive it was revolutionary enough to surrender — and the rest of the world — who might not heed its warning and avoid wars in the future.)

Night bombing during the war was accomplished using radar guidance, but the expected error was indeed on the order of a mile or so. If you were using hundreds of planes, like they did with firebombing raids, that was no big deal: most of them will destroy their target. But with one bomb, it's a very inaccurate way of doing things.

So it was part of the strike order that the weapon be sited visually. That requires a daylight raid (Japan used blackouts during the war, so it is hard to see precise targets). In the end, it is highly likely that they used radar bombing on Nagasaki anyway (and indeed did miss their intended target by about a mile), because of cloud cover.