I have used both. There are definitely times when a shuttle shift will outshine HST, and like has already been mentioned, those times include plowing, mowing, brush hogging, and other ground engaging tasks. I do feel that shuttle shift puts more power to the ground than HST, hands down.
But for the convenience of operation, and the lack of fatigue associated with shifting, HST is the winner hands down when it comes to overall usability.
As for the whine, I noticed it often on my previous tractor, a 23 HP Kioti CK20. However, on my current tractor, I ONLY notice it if I'm in Hi range and bogging down the hydraulics.
Doesn't bother me much tho.