Going back through my DD history-all of my cars('94 Maxima, the LS, and the MKZ) have had moon roofs. The Maxima one was aftermarket.
In any case, given the option of identically equipped cars but one with and one without, I'd choose without for a couple of reasons.
On a practical level, I never use them. To me it's all or nothing-I'll drop the top on the MG rather than getting just a little overhead from an opening in the top. Also, this has never come up in any cars I've regularly driven, but I'm a tall guy and I've been in small cars where the extra inch the roof eats up makes head room a bit snug for me.
My LS leaked. There was a known issue with them where the rubber hoses connecting to the drain would shrink and pull loose. I fixed it myself a few times, but it was a struggle and got worse as the car got older(access was poor unless you dropped the whole headliner-something I didn't want to do). Finally, my mechanic did SOMETHING and it never leaked again. In any case, it would start as a slow drip but heavy rain would have nearly a constant drip on my left leg when driving. It happened on both sides, and got a few of my passengers also.
They're popular enough that it can be tough these days to find a car that offers one as a option and doesn't have one. I've also seen cars where it's not even optional.
The last car I seriously considered buying new was a Chevy SS. The options are few on it, but I wanted a manual with no sunroof. That particular combination would have likely required ordering.