I don't think you recall how Man of Steel went down. Per Wikipedia: "While following Clark, Lois inadvertently triggers the ship's security system. Clark uses his powers to rescue Lois before wearing the uniform and testing his flying abilities. Unable to convince supervisor Perry White to publish an article on the incident, Lois tracks down Clark back to his family home in Kansas, intent on finding the truth. She tries to persuade Clark to let her reveal his story, but decides to drop it after hearing of Jonathan Kent's sacrifice, and keeps Clark's identity safe."
As I recall, MoS Clark didn't start wearing glasses until the end of the film, when he started working at the inexplicably-no-longer-destroyed Daily Planet office. Lois knew of his powers well before then.
The one screen Lois who did see through Clark's glasses, as far as I recall, was Margot Kidder's Lois in the Donner Cut of Superman II.