[f5fstop]

Never heard the expression "drain cups," but possibly part of a drain hose has that description in the parts catalog.
All sunroofs, except for the aftermarket flip up ones, have some sort of drain system. All GM sunroofs I have seen have four drain hoses. Two down the A-pillar, and two out the rear. In the Hummer, both the rear hoses run in the C-pillar, which is the pillar behind the rear door, just in front of the rear side windows. The rear hoses exit just in front of the rear tires.
The drain hoses are necessary since to seal a moving pane of glass is hard, and in most cases, water will not enter the trough for access to the hoses. However, the hoses are there, just in case. In addition, if you forget to lower the rear of the sunroof and it rains, most of the water will drain out (I know this from previous experience).
Usually, what happens is someone at the plant incorrectly routes a hose, and it is routed inside, versus outside. So, water will leak inside. This is a rare type of leak.
Not sure why it is taking so long, unless they had to order a hose. Sometimes during assembly they can be damaged.