Because it's designed for a hot, metallic jet at 400knots, at several miles away. How radar reflective is latex or whatever rubber makes up these balloons? How hot is the payload? If you make the heat-seeking missile too willing to lock onto low grade heat sources, it might suddenly decide that a bird is a better target at the wrong time.

For radar guided munitions, the surface you are targeting needs to reflect enough of the radar energy for the seeker head to "see" it.

Also is the AIM-9X really only $400k? That's insane for the capabilities it has.