Disclaimer: If your Scooter is a 2-stroke the exhaust is complex, none of this may apply, and I have NO experience with them.
The stock exhaust allows for the volume of exhaust at peak power RPM to exit the engine at the velocity designed for optimal engine operation. However, if the volume of air/fuel entering the engine is increased by lets say a high flow air filter, then the increased volume requires a higher volume output. In other words, If you have not changed the intake then the exhaust will not give you more power which equals speed.
If you change the intake volume the carburetor must be re-jetted or the engine will run lean and may seize.
Does the bike have a Tachometer to read RPM? A Tachometer can be added for as little as $11 and is VERY helpful in tuning the bike for performance.