I don't think it was ever implied that women didn't use makeup during the TNG era. The impression I got was that it was a lot BETTER kind of makeup that didn't require all that touching up and so on that we have to put up with now. Don't even
get me started on lipstick...
Anyway, I'm thinking in particular of the episode "The Outcast" - the one with the androgynous species. That includes a brief discussion on cosmetics between Beverly and Soren, and it's clear from the conversation that Beverly takes it as a given that many human females, including herself, do wear makeup.
But as for the bad makeup, they just used waaaaay too much on most/all of the female actors, and it was the really obvious sort of makeup, with enough blusher and bronzer to coat a battleship. (Apparently they had never heard of the natural look?
) I noticed it even at the time of the original broadcasts.