Nah, it's just that they say it all bloody day long; it becomes a Pavlovian response after awhile. When I was a clerk, I can't count how many times there were when I'd say, "Thanks for shopping at---," and the customers would reply, "You, too!" And then they'd pause for a second, blink, and say, "Uh, I meant, 'Thanks and have a nice day."
They were so used to clerks saying "Have a nice day" that they automatically answered, "You, too," just because that's what they'd always say. It's just habit.