The first step in doing make-up is applying a foundation to even out the skin tones for the camera. So pretty much every square inch of visible skin is going to made up--face, nape of the neck, and hands. (This will, of course, require a lot of make-up if the entire upper body ends up having to be made up for the cameras--when an actor goes shirtless.)
Having applied make-up to the entire upper body and having evened out the skin tone, the make-up artist then needs to decide if he's going to go back over the nipples with something akin to lipstick to make them standout again. It would be very easy to go overboard and make the nipples overly cartoonish and freakish. Probably easier to not highlight them at all and let the only distinction between the nipples and the rest of the chest be the slightly different skin texture, instead of the pigmentation/coloration.
So the make-up artists don't actually "cover the nipples" and the nipples aren't "unnaturally pale;" rather, make-up artists actually cover everything, and the skin is all unnaturally even-toned. (The make-up artists simply don't bother doubling back to re-emphasize the nipples with additional make-up.)