The three inch straight through exhaust input in my car made it sound faster- it made less power on the dyno though.
The props may be spinning faster as they have less thrust for a given rpm...
The intake is tuned to control the speed and vibration of the air. As it works with things like intake runners,injectors, valves and so on.
Think of it like a trumpet.
You change this, the air changes frequencies and then no longer works with the oem system. Nothing is no longer matched and the injectors have issues with atomization of fuel. Hence the decrease in performance. The air can be tuned back by adding a few bits. This same issue can cause issues with MAF readings to the ecu as well.