This was an interesting discovery, run into a couple years back when I was performing a home inspection. I was out by Lake Whatcom at Sudden Valley. The home was relatively new and it was situated in a heavily wooded area with tree needles and heavy limbs all around and over the roof.
As I got up onto the roof, I was surprised to see an extra skylight. In a quick preliminary perusal inside, I had seen two but not three. Then as I got over by one skylight, instead of a view down into the house, all I saw was the back of batt insulation. They skylight went nowhere. Sure enough, this was some type of builder's error, oversight or impractical re-design. Either they forgot the shaft, or they decided against it using the skylight after it was cut and installed at the top side. As it was, back behind the house, with the tree canopy above, nobody would have realized it was abandoned from inside the house or from the grounds below.
I thought of this as a sizable deficiency. Skylight installations have been known to leak. And the idea of all these heavy limbs near the skylight, and nobody having a view below it from inside -- till water seeped into the attic and out through the ceiling -- was unsettling. The abandoned skylight is more vulnerable to leaks, fallen limbs or broken glazing, than the roof itself.
I do not know how this all turned out, I assume the clients bought the house. But I recommended to my clients that they have a roofer remove the skylight and patch the remaining hole. The other option, of course, would be to put in a skylight shaft -- if it was possible to do so. I am assuming there is a reason why the contractor bagged the original plan in the first place.