I used to query flagged comments from time to time using the API, just out of some morbid curiosity. It definitely used to work for that; I am not sure if flagged items are in the same class as dead ones, though, or if they have since deliberately eliminated this capability. I eventually found more interesting things to do :)
The problem was that many third party apps and clients were displaying flagged and [dead] comments as if they were normal comments. Then we'd get angry emails about all the horrendous comments we were "condoning" when in fact the users posting them were as banned as banned could be.
