For the last 15 years or so the M61 combat loadout has been 100% semi armor piercing high explosive incendiary. A balloon skin is not going to create near enough resistance to cause the zirconium component to ignite the explosive / incendiary compound, so you're just punching (kinda big) holes.
The main problem with using that kind of ammo over the continental US is it does not have a self destruct function, as do some 20mm rounds, and so you're going to spray potentially dozens of bullets which if fired from 60k feet will ultimately fall to the ground and explode after traveling a VERY long distance, potentially injuring people / property and starting wild fires. The risk of most of that is next to zero over the ocean, naturally.
An AIM 9 makes better sense over terrain, as not much is going to make it to the ground, and what does is going to be quite inert / spread over a very wide area by the time it reaches earth.
It would be possible to swap in some of the self-destructing ammo like is used in the Phalanx, but it's not going to be ballistically matched to the targeting computer, possibly making the predicted lead and drop be quite a ways off. All that being said, you are overstating the size of the bullet hole in a balloon. 20mm is roughly 3/4 inch. Dozens of holes of that size in a balloon the size of several school buses just doesn't amount to much. As compared to a high explosive missile warhead projecting a radial fragmentation pattern that's designed to cut through airframes at hypersonic velocity? The bullets holes are tiny in comparison.
There will however be much more balloon material left over after whacking it with an autocannon, creating a drogue / streamer effect, greatly reducing the terminal velocity of the unit, increasing the odds of recovering it in one piece dramatically.