I understand it is a core mechanic as a means of levelling up. By mid-game the open world option of gathering them becomes almost pointless when you consider that you can acquire 300+ with one quick random encounter, blasting through enemies. I also think they ruin the scene, personally. Maybe an option for just Timed orbs and Airways to be visible, so those Rainbow and Multi-colored Z-Orbs are still easily attainable.
This would really improve the endgame experience. I don’t see it as likely, making them invisible might work – but the sounds and quotes would persist. I’ll look into it sometime soon. Don’t expect much from me though ^.^