EarnestDD,
"When you get improved fuel economy you normally also get decreased emissions since the fuel is burning more completely."
Normally, when the combustion efficiency, think thermodynamic efficiency of the engine, increases, so does the NOx emissions.
In this case, the aero muffler would not increase the thermodynamic efficiency of the engine, but, would improve the volumetric efficiency somewhat. When that happens the catalytic converter becomes slightly less efficient as the exhaust gas would have less residence time in the converter. Therefore, I would expect the emissions to be slightly worse without recalibrating the engine's computer control system.