If the poop is blocking the vents, you do need to clean them. But spot cleaning is better than dipping the chicks in water and getting them all-over wet.
Placing them in the incubator to dry is a good idea, but a hair dryer on the lowest setting won't bother chicks if you understand how to approach them with it. The secret to using something noisy around chickens of any age is to turn it on while you are still a good distance from the chicks. Then move closer slowly with the noisy appliance, and by the time you get into close proximity to the chicks, they won't even notice the noise.