If you keep the motor the same and just increase the voltage, the motor will be able to spin faster. This may put you into a situation where the motor wants to go faster than it can really go due to wind resistance. You might get full speed on a steep downhill, but on flat ground or uphill, performance could be much worse if the motor is outside of its efficient range.
It is important, therefore, to try and match the motor gearing and voltage so the top speed is still in the efficient range (unless you are racing).
In comparing 48v, 40 amps to 72v, 20 amps, if you are using the same motor, the 72v case may or may not be more efficient. At higher voltage, there will be less resistance losses in the battery wiring for a given power level, but that doesn't amount to much in the first place. In the 48v case, the controller losses will likely be less, which also should not be much.
Keeping the motor efficent is generally much more important than keeping the wiring or controller efficient.