She came out of the room with misted glasses.
Is "misted glasses" natural to use to say that she had been crying and maybe still is? Is "misted" the best/correct word to use in this context?
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I wouldn't understand the implication. Misted glasses occur when you are walking in cold rain or sometimes when you move from a cold to warm room. Glasses don't get misted up from crying (at least not in my limited experience of glasses — or crying)
"Red eyes" or "running mascara" are possible to imply that someone has been crying (although the first could also just mean "sleepy")
However google books does indicate a number of examples, mostly from romantic liturature:
... she had taken off her misted glasses ... she had cried so much she could not be goaded to any more tears (Joy and Josephine, Monica Dickins)
His glasses were misted with crying, so he took them off and peered at me (Who calls the Tune, Nina Baldwin)
So "She came out the room with glasses misted from crying" might suit your purpose.