Most weather balloons are small. The balloon is 3ft across at the ground. The payload is phone-sized or computer-sized. The payload wouldn't be visible to fighter.

There are large scientific balloons. I couldn't find any standards of large balloons using transponders. They have communications and tracking so location is known. I wonder if NORAD is in contact with all the organizations about their balloons.

I suspect there will be move to put ADS-B on larger balloons.