What is the model and year of your bike and what muffler are you using? I would be careful about make a change that cannot be reversed. The standard Honda exhaust is highly tuned. You may not like the result of your modification.
If you shorten the pipe, you will be moving the peak power up the RPM band. The intake side is also tuned. The intake, exhaust and cam profile are designed to match.
The intake and exhaust are timed to the four engine cycles. On the exhaust side: when the valve opens a pressure pulse shoots down the pipe, when it hits the muffler (usually referred to as the collector) a low pressure pulse shoots back up the pipe. If the low pressure pulse hits the exhaust valve at the same time as the next valve opening, a supercharging effect happens.
The same things happen on the intake side. The difference is the air/fuel travels down the intake tract it is interrupted by the valve closing. When airflow stops, it builds up pressure. If the peak pressure hits the same time as the next valve opening, a supercharging effect will happen.
The longer the pipes (intake tract and the exhaust pipe), the lower the peak power occurs on the RPM band. The shorter the pipe, the higher RPM the peak power happens.
The length of the power pulse determines how wide the the RPM band (low to high) is when the super charging effect happens. A smaller pipe has a longer pule. A larger pipe has a shorter pulse.