I mess with mine--take out shells, candle some I'm worried about, take one out for a cuddle... it doesn't seem to cause any problems. The humidity rises during hatching even without additional reasons, just because the chicks are wet. If you have condensation on your incubator's lid, go ahead and take the hatched chicks to the heated brooder. They will not dry in the incubator. I wipe down the lid and even sop out water from below, with an old t-shirt, etc.
Your hatch delay might have been caused by lower temps earlier in incubation. If you haven't calibrated or found the necessary correction with a calibrated thermometer, you should look into doing that. Incubator thermometers are sometimes calibratable, but seldom accurate without calibration.
