The difference in the Juggernaut HD and Juggernaut Ultra is two-fold:
The motor systems differ by the way they deliver power.
The HD uses a more basic system of cadence sensor(how often you pedal) whereas the Ultra motor uses a torque sensor (how hard you push on the pedal) and a cadence sensor. Thus, the Ultra motor delivers power with a more natural feeling.
The torque sensing is a more complicated system so, therefore, it comes with the added price tag.
The Ultra bikes have better base specs like standard hydraulic brakes and thru-axle rear hubs.