To mate megaphones and CIS requires some air/fuel adjustments, I believe. It's also the same when going from heat exchangers to headers.
I've debated megs and came away with they being inappropriate for street driving when you need low and mid-range torque. Megs seem to sap that as they're truly for WOT racing only.
And as others have said, they're too loud for the street. I've heard sports mufflers, and they seem no louder than many others, plus preserve the torque band.
At any rate, megaphones are even illegal on some tracks because of their loudness.