At a given power input, the higher voltage would have less current going in. Since this would decrease the energy loss for the battery and controller's resistance due to the lower current flow(P = I^2*R), the system would be overall more efficient at a given power output assuming every other effect is negligible. Since this would indicate a greater power output, you'd be going at a greater speed which also has the effect increasing cogging torque, so this would pose an efficiency reducing effect.
I should just bring up the formulas so everyone can eyeball it and spot things I'm not thinking of.
Now that I'm looking at the formulas, I'm realizing it's not as simple as looking at one formula. The existence of two separate regions(current-limited and throttle-limited) impairs the discussion a bit as there'd be three separate cases at a given speed with everything else equal:
where v2>v1(both different voltages)
1)
v2-current
v1-current
2)
v1-throttle
v2-current
3)
v1-throttle
v2-throttle
For the sake of discussion, the controller limited region suppresses efficiency. You'll notice the "bump" in the efficiency graphs at ebikes.ca's simulator(and my vehicle simulator) when passing from the controller limited region to the throttle limited region.
Here's the code for the simulator's core which contains the fundamental equations if anyone cares enough to deduce the needingly complex answer to this question.
http://svn2.assembla.com/svn/ebikecalculator2/EbikeCalc2/src/ebikecalc2/Motor.java