A lot depends on the color. Some cover better than others, and counting coats doesn't ALWAYS guarantee you'll get exactly the same paint thickness and coverage everywhere. This can even be a problem on 1:1 cars...it's not unusual for a hyper-critical old car-painter like me to spot a slight mismatch between panels on just-finished showcars.
Ideally, the hood should be in place when you shoot the color. This can lead to more problems if the paint gets into the seams and sticks the hood shut...causing a real mess when you try to cut it free.
If you're going to use a clear top-coat, shoot your base-coats with the hood in place to assure even color, and remove the panel to shoot your clear.