Well according to the Ralbag they really couldnt breathe:
The Ralbag on Choshech quotes the Medrash about the darkness being a golden coin thick and explains that the darkness was tangible and so strong that the Mitzrim were forced to plug their nostrils and mouths up and it caused a tremendous suffering. If the air would enter their bodies they could die.
The Bal Kesav V’hakebbalah takes issue with this pshat and asks how it is possible to survive with their nostrils and mouths plugged up for three days.
