While developing the BrickPi3 I did extensive testing with 12v connected to the BrickPi3 running Lego motors (primarily NXT motors, but some with EV3 motors). There were times that the internal PTC re-settable fuse tripped and had to cool off, but I didn’t notice any degradation of the motors over time.
The motor speed/power is controlled with PWM (Pulse Width Modulation, which is switching a constant voltage on and off rapidly). On the BrickPi3, the PWM frequency is 20kHz (fast enough that you can’t hear it “hum”).
Honestly I think the most likely problem would be that the extra torque could cause gears to strip prior to the fuse tripping, but I’ve never had it happen to Lego motors (and I’ve used them a lot). You could limit the PWM to something like 75% to reduce the likely-hood of a mechanical failure, but I’ve never worried about it, and I’ve never had an NXT or EV3 motor fail.