I don't think this is at all the same technology as is used in anti-theft tags (which, you are correct, could be rendered inert this way).
The RFID tags I've seen from 1990 on generally store energy from a received RF burst and emit an RF signal, typically conveying a fixed unique N-bit code. A microwave oven *might* damage these; a mini-EMP generator could also (I am guessing).
Like I said, a hand-held bulk eraser -which is just a rudimentary EM generator - should fry the bejeezus out of any chip if you hit it long enough. I'd think it would scramble the eggs of any data coded into it.
