Anytime you modify an exhaust system you are affecting the performance. The thing to remember is the manufacturers have to design an engine with noise in mind and so, the engine tune is matched to be the best it can be with that particular exhaust. The engine can be modified to perform better IF you change a combination of items so that they match (jetting, intake, fuel maps, etc.) the new exhaust design once baffles are removed.
Most people just want the noise and think if it's louder it must be faster.
Now, on 2-strokes, the exhaust design makes a HUGE difference! That is an art/science unto itself!
On the other hand, with a turbocharged engine, everything after the exhaust turbine is irrelevant and unnecessary. A short open pipe is best for performance and usually is not much louder than a standard engine with a muffler due to the turbine breaking-up the exhaust pulses.
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