Firstly, it's important to recognise that it's Watts that you really care about.
Watts (W) = power
Watt/hour (Wh) = capacity
.....and.....
W=V x A
This means that a 48v battery running at 10a is producing 480w. A 36v battery running 13.3a is the same amount of power.
Assuming both motors are wound proportionally similar, there's no difference. Same power, same speed (so the same torque, since P = S x T).
...however.....
If you run a motor designed for 36v at 48v it will spin faster, and consume more power. Assuming it does not fail due to excess power, it will consume the battery capacity faster. It may not operate in its most efficient zone, wasting power as heat.
In practical terms it's a bit of a compromise, and 36v is where most commercially available machines have settled.