"Little lady" can indeed be a term of endearment, but it can also be somewhat derogatory, or sarcastic. Depends on the context, really.
In a postive way, "Little lady" is often used in show-biz, like people on stage. As in "A Big Hand for the Little Lady." (a movie from 1966 with Henry Fonda). Or, at a fair, the guy at the stand might say to a man and his (younger) daughter: "Here's your bear, Sir, and some candy for the litlle lady."
"Little lady" can also refer to one's wife. As in: "I brought back some bacon for the little lady."
Derogatory/sarcastic:
"Where do think you are you going, little lady?"
Which is what a father might say to his teenage daughter who want to go out late at night. Americans slightly favor "young lady" in that case. Like I said, much depends on the circumstances, really, whether the person is being sarcastic or not.