You have to turn the keyed ignition off any time you walk away from your steed, and take the key with you, so from that standpoint it doesn’t matter if you stop the motor with the handlebar kill switch.
Having said that, when I ride one of my two wheelers and it has a handle bar kill switch, that is how i stop the motor, then i turn the ignition off and remove the key if I leave the steed unattended in a public parking area.
Another benefit the handlebar kill switch affords is the ability to quickly stop the motor, w/o removing your hand from the hand grip.
One disadvantage to using this switch instead of the key only, if you turn the motor off with the kill switch and forget to turn the ignition off with the key, you will drain the battery flat. i know, I’ve done it many times on various two wheelers, including my Super 9, and i did it quite a few times with the People 150 I used to own/ride.
Both those scooters, the head light only turns on after the motor is running so stopping the motor with the kill switch and leaving the ignition on with the key, the head light wont stay on to remind you to turn the key to the off position.