I keep mine in the Apple Leather Sleeve--there is a little click when I take it out of the sleeve and/or open the lid, and I think I figured out that it's just the little separator kind of sticking to the metal and coming undone when it's not in the sleeve, which is a pretty tight fit, even on the Air. If my laptop is just sitting there closed on the table and I open it, no click. It's only after I take it out of the sleeve. It either makes the click sound right away, or it does it when I open the lid.
I'm not worried about it. Nothing is loose or malfunctioning. The lid is nice and solid when I adjust the angle or open up the computer. There is no flexing or weird noise in the keyboard or anywhere else.
I remember my old Macbook Pro with Retina display used to have an issue where there was some kind of plastic sheet inside the screen that shielded the LCD from the rest of the lid, and it would invariably come loose on all of those models. If you moved the computer from side to side, you could hear it sliding back and forth inside the screen. I considered that a far worse problem than this little noise my current Mac lid makes. I think it's just a humidity thing.