Jumping seems useless and all, until get nailed with a wall of grey notes, and you don't want to break your clean streak. Essentially, it's either use the jump ability, or clear the grey blocks you've hit, and if you're going for the stealth bonus, you'll want to use jumping more. Although jumping does mean you'll hit less notes, which potentially screws you out of the butter ninja/seeing red bonuses. Not to mention match21 (which is mostly impossible anyways, I've only managed it twice on Ninja Mono).
PS I'm 7th right now on through the fire and flames >:V