They make a little paint thickness reader. I had one when I was in the car business. If I was at an auction I could tell pretty quick if there was mud in a car going across the block. I don’t remember the brand or the cost.
Taking a look at the back side of the panel will give you an estimate. If you can get your hands on a borescope inspection camera you can usaully get in to the rear of most things......
Magnets work well for non destructive checks. A test on known painted surface without bondo then try on a panel to see how it compares. Wont tell you exact thickness, but will tell you if there's much bondo.
They have cheap versions that look like a felt pen, and they make digital ones. They are made for reading paint thickness and I have seen guys use them prior to cutting and polishing older paint jobs. Not made to measure filler, they can do so if you read paint thickness on a panel that you know has no filler (like a hood or gas door). Then read other areas and deduct the measure of the paint. That should leave you with your bondo thickness.
When the debris changes from white powder to metal, STOP drilling, mark the drill bit, remove from hole and measure how deep the bit when in before it hit metal.
If you are re-painting the car. Doesn't really matter. You will be removing all of it, regardless of how thick it is. If you are going to refinish it correctly.
When I was about 15 and looking to buy my first car, I made this electronic gadget which had a small (1"x1") transformer on a lead , and plugged into a small circuit which had an earphone. It worked like this- you held the transformer against the panel, and the distance that the metal was from the surface would change the pitch of the sound in the earphone. It was built from a circuit from an old electronics magazine, but shouldn't be too hard to find or design. The transformer was re-configured to suit, and had a layer of tape over it, and I had it mounted to a finger ring. With a little practice you could work out how thin or thick the layer of bog was.