Um, no. The only difference between jump shrugs and jump squats landing (with a barbell) is that one has the mass centered above the shoulders (jumps squats) while the other has it centered below in the hands (jump shrugs) with good landing mechanics to absorb said force of course. By the time you hit the deep squat (if you're even going to deep squat), there should already be significant deceleration where the loading on the rear surface is minimal! It's not like with a jump squat were going to accelerate down to the bottom and stop to absorb all the force at the bottom, heh.
Heavier load is a valid point, but you can easily negatve that by dropping the loaded weight from the jump shrug while you can't with the jump squat. Plus, again you get the feel of actually doing oly lifts in the first place.