The factory white sunroof graphics are not perforated. I don't know how much light they let in though--haven't seen them from the inside looking out.
The disadvantage of the perforated graphics is that you can see the perforations at close distance--not really a big deal--but they also will appear lighter at a distance than the nonperforated graphics. Look at some cars with sunroofs that have full checkers (not on just the sunroof, like Jwardell's, which incidentally is a very sharp looking car), if the sunroof is perforated, it looks different from the surrounding graphic; if it's not perforated, it pretty much looks the same as the surrounding graphic. Go to Coopersflags and look in their gallery--you'll be able to see what I mean. They may have some pictures of a perforated white sunroof versus nonperforated too--you'll see the difference.
Personally, I'm going to go with a nonperforated (factory) white cover--I think it looks much better. But if light is the overriding factor, I'd go perforated.
JWardell's car is a nice compromise--by getting the checkered, perforated graphic on the sunroof only, there is no discrepancy between the checks on the sunroof and the checks on the remaining roof. This looks better much IMHO than getting the entire roof checkered and using a perforated graphic for the sunroof (although getting the whole roof done and using a nonperforated graphic for the sunroof looks great too).
Hope that all made sense....