I’m sure this has been mentioned, but it seems if a spy aircraft with a visible payload from an adversarial country invades our airspace, threatening our national security, wouldn’t the Secret Service/military have immediately called for the President and Vice President to be taken to safe bunkers? Obviously, it wasn’t much of a threat.
Depends on how you define "air space". They don't hustle officials into bunkers every time a Chinese satellite goes over, so "air space" only goes up so far.
The concern the military has with the region above the air space has only been for ballistic objects, including those entering from space. For intercepting ballistic objects they have big expensive missiles on bases which would not be appropriate to fire at balloons over the US in peacetime.
Balloons fell through the cracks. It would be expensive to track them and devise a new system to bring them down from extremely high altitudes (well above 60,000 ft), and the military has other priorities.