Hydraulic disc brakes are a total overkill for anything but downhill racing and they're pain in the butt to maintain and repair. There will be no benefit whatsoever on a commuter bike. These mechanical brakes are fine. I have really cheap Hayes disc brakes and they work just fine on my commuter: they give me enough control and yet are powerful enough to lock my wheels at any speed with loaded panniers. I wanted to replace them with Avid BB7s but they really work fine.
I actually wouldn't get the Kona because of this, I prefer mechanical disc brakes actually for their simplicity and reliability.
A.