Greetings:
Pulsations mean the braking surface is out of round (drum) or out of true (disc) There is no other explanation. In cars, it's sometimes the result of haphazard torquing of the lug nuts or bolts. Overheating on scooters - perhaps long downhills with the brakes applied - could explain the reason.
The pads or shoes "wearing in" will not compensate for this. The risk in mild cases is minimal. In the most severe cases, firm application of a drum brake in particular could cause wheel lockup in a panic stop situation. This could lead to Serious Injury or Death.
Drums and brake rotors can be turned or trued on a lathe if suitable equipment can be found, or replaced if not. I've had to replace a few Honda 50 rims over the years for this reason. Stock steel rims have 95mm drums built into the hub with a couple of my builds capable of speeds over 70 MPH. One hard stop from over 60 can distort a drum. New rim solves the problem immediately.