Radars can pick up balloons just fine, so long as they have sufficient sensitivity and so long as the tracking algorithms are tuned recognize such slow movers as something to track. (The material of the balloon envelope doesn’t have nearly as much to do with it as you seem to believe.). But, none of that really matters very much with the missiles in this case, since they have IR seeker heads (a.k.a. “heat seekers”) rather than RF (“radar”) seekers.