I have the K&N FIPK2, aftermarket muffler (performance), and 2.3" pulley on my 02' supercharged X, all with no problems for the supercharger.
As far as too much airflow causing problems with the supercharger...there is nothing there for a reduction in inlet restriction to damage.
FWIW I gained about 1Lbs of boost by switching to the K&N filter.