I know the Asus manual says it needs stock heatsink, but having used it, I can't see why that would be the case.
CnQ does not appear to affect the speed of the cpu fan; it does not vary voltage to the fan or anything like that. However, it DOES underclock the CPU by switching to a lower multipler (on-demand) and correspondingly cuts voltage to the CPU. When the demand for more CPU resources are there, it switches the CPU back up to it's default multipler, i.e. the highest available on the chip(1).
1 = note that this may cause problems with your overclock if you are running at less than the highest multipler, i.e. 9.5 x 250 on a Newcastle 3000+.