It matters a bunch. All kinds of noise can get picked up over cables and bleed into your audio path on a digital rig. It happens all the time just with power cables which is why every musician carries a handful of "ground lifts" even though they're technically illegal in a lot of places. That said, MIDI over USB is kind of necessary in this day and age. Hopefully instrument manufacturers will be rigorous about isolating any interference it could pick up.
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