I'm sure if photographs had existed at the time, we'd see what their faces really looked like. As another person here said, people painted the ideal, and would usually smooth over any major... flaws in the person's appearance. I mean if a person is paying you to paint their picture, are you going to make them look ugly?
In terms of actual proof, here's a scientific article about acne treatments that references treatments dating all the way back to good old Ancient Egypt.
I'm no historian, but I've been told on several occasions that artist often were trying to depict an ideal, not necessarily reality. Also, if a work of art is commissioned, I would assume the painter might try to make the subject look good so that they are happy with the result. Hopefully someone more knowledgeable can step in here with some more facts and sources.