When I wrote my last post I had both stator and SKF bearings ordered. The old bearing had very subtle freedom of movement when I aggressively moved the wheel in the direction of the axle.
Yesterday I finally got my SKF bearings and sat down to open the motor. As Bikemad predicted it was a mechanical issue. It was obvious the stator was gently rubbing the magnets at 2 points. The stator has no cracks or visible bends (Aluminum breaks. It usually doesn't bend).
At this point I decided to throw the dice : I replaced the bearings and left the old stator.
The result was an improvement from having the noise 10% of the time to just 2% of the time. There is also a significant improvement in torque and accelerations.
The million dollar question now is whether this friction will decrease once the touching metals will erode or will increase since something is not straight (stator axle, stator wheel). In any case a new stator is on its way to me. If situation gets worse I'll replace both motor and bearings.