If you are going for differential pairs, then I wouldn't worry too much about what voltage the differential pair is running at. 5V is prefectly good for differential systems, as that's voltage what most modern CNC encoders operate at.
The key feature of differential pairs, is any noise that gets picked up, should be cancelled out by it affecting both wires by a similar amount and the differential voltage remaining reasonably constant. (This is a very basic explanation, which I'm sure Jonathon will criticise me for it!)
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If you're running single ended, then yes, a higher voltage is better, which is why industrial machines nearly always run 24V control systems.