If the agent being winked at was the one who did the extra screening, I could offer the following scenario: she thought the winker was also cute, and was hoping to strike up a conversation during the extra screening and maybe get asked out on a date.
[Most of the female agents i've seen are not cute--but there have been exceptions. Once I arrived at sfo (at a very slow time), when I got to the checkpoint, there were two female agents, nice looking, and I was the only one being screened, they both said "the gate is closed..." as a joke.]