I have the same thing on my own and can confirm a friend's AK 550 also has this.
Both scoots have around 30K km on the clock and 2017 model.
These vibrations you describe come around 50km/h +/- 5km/h and they resurface at around 100km/h but in a somewhat lesser way?! (Or less pronounced because of noise/wind speed)
New tires, correct tire pressure, new CVT belt changed nothing.
Final drive belt still from factory but tension have been checked by dealer, still no improvement.
Brake discs and pads ok on front, rear disc has some wear (perhaps parking brake induced?), pads move freely. Fluids bled and replaced.
I am thinking of checking wear on rollers, the part of the variator housing the rollers, variator sleeve/boss and/or replace.
Friend's AK has a Malossi variator fitted but these harmonic vibrations where there with the factory variator and also present after the Malossi was fitted.
So far we could not find the source of the problem.
I am trying to think it is the nature of the beast, but I wish it would run smoother.
Let us know if you find anything.