I think there is a very good chance that McGonagall is worried enough about Hermione, about Dumbledore, ... and won't check Harry's Time-Turner. She's not much into multilevel plots, she's smart, but too honest to live in constant suspicion.

Like she didn't think much about the consequences at the "war level" when she offered the fealty oath to Hermione back then in the Wizengamot.

She sees Harry in pain and traumatized, and she sees the immediate chaos, it wouldn't be very "in character" for her to suddenly suspect Harry and probe him like that.

It could happen because she learned to not follow her "role" anymore, but it still doesn't seem the most likely thing for her to do.

Moody or some aurors on the other hand...