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What, exactly, does Ninamori mean by expressing that "They're fake"?
Her finger is through the lens in that scene; Ergo, they're props.
It seemed to me to be a subversion of the standard "character learns an important lesson and so becomes more at ease with their self" plot. Usually said character would wear the glasses she'd kept secret, but Ninamori is still childish, if not more so - she keeps the lead in the play even after being called out on it and continues to wear contacts. In fact, maybe the glasses were never real in the first place and were just a way to trick Naota into thinking she's more grown-up than she actually is.
Nah. You can see the light reflecting off of the lenses when she's wearing them in Naota's house.