I doubt a balloon with a circuit board could cause an engine to fail, but there are lots of sensitive measurement devices, like a pitot tube, that I imagine could fail if a balloon hit it. (For reference, Aeroperu 603 was brought down by tape that wasn't removed from the plane.)
I'm all about hobbyists hobbying, but it does seem like there should be at least some so of registration system so we know what people are launching into shared airspace.