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I think we can safely forget about the chances of spyplanes hitting balloons, the volume of space versus the number of spyplanes would make that a non-issue, even if there were a lot more balloons.
So 35000 feet (11 km give or take) would be a reasonable upper limit. Let's assume the worst and start from 0, you have a shell above the earths surface up to 11 km above it, which has an approximate volume of: 510.1 million km x 11 = 5610 million cubic kilometers.
That's a lot of space. Every cubic kilometer is 10^9 cubic meters, so 5.6x10^18 cubic meters.
I don't know how many aircraft are typically aloft, but let's say it's 20,000 craft and they're all of the very largest variety (say A380, or Boeing dreamliner). They're approximately 60 meters long, and 6 meter in diameter, so that's 1700 cubic meters, let's double that to include the wing volume, so 3400 cubic meters.
We have 20,000 of them, they're all aloft at the same time, so all the planes take up approximately 68,000,000 cubic meters.
Now for the balloons, they're 10 meters in diameter, worst case they are 50 meters high or so (instrument package dangling below the balloon, assuming a cylinder with a radius of 5 meters and a height of 50), so about 4000 cubic meters. ('assume a spherical cow of uniform density').
So how big is the chance that one balloon intersects in all of space with the volume of all the aircraft given that both have all of the atmosphere to play cat and mouse in?
68,000,000 / (5.6x10^18) = 0.000000000012 (the chance that any given cubic meter is part of the space occupied by an aircraft) multiplied by 4000 (the number of cubic meters in a balloon) is about 0.000000048. So that's pretty small but non-zero, multiply by the number of balloons aloft at any given time, but keep in mind that most of the factors here were taken very pessimistic (as in, favouring the collision). The calculation also totally ignores the relative speeds of the two types of vehicles, ascent speed of balloons, the time factor, ability to manoeuvre and so on.
See also:
http://weatherjackwilliams.com/answers-weather-balloons-and-...
edit: extensively edited after avoid3d spotted a crucial error in the math, I had dropped 6 orders of magnitude.