Ripley says in the inquiry in Aliens
that Kane "said he saw thousands of eggs there...thousands
", implying that the Exec relayed that information (at least to her) in the hours between his re-awakening and his death.
Wouldn't that suggest that Ripley knew about the eggs? Maybe not so much of a leap for her to see Brett's state and connect the dots. After all, she did complete the Company's Horizon Beyond OTP with honors.