Matt, I have absolutely seen aircraft interrupt a microwave path. This is actually a fairly common occurance near airports and runways. We've seen it with helicopters also. There are two likely scenarios; what I would call 'direct' line of sight (LOS) obstruction where the plane actually flies into the 1st fresnel zone and 'incidental' where a reflection of the signal off of the plane causes fading and/or bit errors. The latter is probably less of a concern and more likely with larger aircraft.
You should be able to map this out. If the plane is literally flying into the main RF path, it is likely to cause problems. Changing antenna heights can help, but the exact interception point of any given plane is probably going to vary slightly. Off topic, but as interesting is interference from wind turbines. That topic is getting a lot of attention in the wireless world right now. Brett 303.317.4449
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