Most probably. If you want to screw with your engine and NOT screw it up, you need to find a source of a good tuner chip and do what it will allow. My son got a tuner chip for his main ride. He did an EGR delete, cat delete, put a huge muffler on it and ran a 5" pipe from the turbo back. He doubled the horse power and kicked up the mileage a little. I can hear him coming home from 3/4 mile away on a quiet day. The factory clutch lasted for a couple of hundred miles and he has put a dual disk clutch in it good for 900 hp and he has snapped off both transmission mounting bolts twice so far.

You would lose all scavenging effects designed into the exhaust.

If you remove the muffler or any other engineered part of the exhaust system you can expect negative effects. Most common will be reduced performance, especially in the form of laggy throttle response. Reducing back pressure will also increase NOx emissions in most cases.