At that point they might remember they have 20mm gatling cannons on the F16 and F22. Not as cool or long range as missiles, but I imagine significantly cheaper to fire in short bursts.
Bullets fired still land somewhere and are difficult to stop once they leave the gun.
The F16 and F22 are somewhere in the 110 to 160 knot range for stall speed. The balloon, for all practical purposes, is 0 knots. Shooting at something straight ahead that isn't moving while you're moving at 160 knots may pose some more challenges than locking into it with a missile.
A zero pressure balloon ( https://www.nasa.gov/scientific-balloons/types-of-balloons ) is roughly equal pressure on the inside and outside. These balloons do not "pop" as such when punctured and may cause additional hazards as they descend uncontrolled.
Hobby balloons, though, are not zero pressure balloons. It's part of how they control their own flight time, by intentionally bursting when they reach a high enough altitude. So a 20mm cannon would probably have a reasonable chance of success, though it would be spreading a lot of lead downrange that would eventually hit the ground, and could annoy people in the path.
these balloons are too high up sometimes to get in cannon range. then there's the question of where the bullets fall after they rip through the balloon, hopefully not on anyones house.
