Getting your ground speed would have been a real pain since you would have to have calculated it from your indicated air speed and guessed at the air density and winds aloft. Or you can time it by using fixed reference points below you... except those were being obscured and are still remarkably easy to get wrong when you're 10KM away.
Still, if you want to hit a target like this, you have to be able to see it, and see enough context around it to be able to recognize it.
_Over Japan, bomber crews soon discovered strong winds at high altitudes, the so-called jet streams, but the Norden bombsight worked only for wind speeds with minimal wind shear. Additionally, the bombing altitude over Japan reached up to 9,100 metres (30,000 ft), but most of the testing had been done well below 6,100 metres (20,000 ft). This extra altitude compounded factors that could previously be ignored; the shape and even the paint of the bomb mantle greatly changed the aerodynamic properties of the weapon, and, at that time, nobody knew how to calculate the trajectory of bombs that reached supersonic speeds during their fall_
This wasn't a normal bombing run. It had elements of an experiment - they wanted to understand how the bomb worked, so they wanted to control the drop precisely and be able to observe the effects.
The aiming points were very precise (a bridge in the case of Hiroshima), and they were chosen well in advance, and the mission orders were quite rigid. If the crew couldn't see the target clearly after several attempts, they didn't have the authority to randomly drop the bomb somewhere else - they had to go on to the next city.
Ironically, after all that, I think they eventually missed the aiming point in Nagasaki by 2 km or so, because it was also obscured. By then, the plane was low on fuel though, so I guess they were forced to do the best they could. I've read that they weren't supposed to do that, according to the mission rules. The plane came very close to running out of fuel, which I guess might have made them drop the bomb to reduce weight.
edit: This is Field Order 13 - for the attack on Hiroshima. It includes Kokura and Nagasaki as secondary targets, so you can see how precise they were about the aiming points. I'm pretty sure the target details would be exactly the same for the Nagasaki attack (Field Order 17, which I can't find online).
https://www.flickr.com/photos/kafaikan/6693719785/sizes/l
edit2: Bomber crew member's diary which explains what happened over Kokura - http://www.mphpa.org/classic/COLLECTIONS/CG-ASPI/01/Pages/CG...
Just thought I'd share some of my puzzlement here; but it sounded as if they'd dropped a third atomic bomb. I though this unlikely, unless the diary is revealing a secret kept (the drop sounds as if it'd failed), but then I came across this: http://en.wikipedia.org/wiki/Pumpkin_bomb
So, in addition to the nuclear models, they dropped identical conventional bombs of that type as well. Never knew that.
You could e.g. read "Target Tirpitz" which is a historical account documenting among other things how smokescreens were used to defend Germany's biggest battleship against a large number of bombing runs. A battleship is pretty much the biggest target you could have on a battlefield, showing that this tactic is very effective against non-indiscriminate bombing.