No, there has never been a report of any harm coming to an iPod during security checks. Metal Detectors, X-Ray machines have no effect on them. Airport security staff may request to see the iPod working, as they now do with laptops and other electronic equipment.
If you have any concerns about carrying it through security place it into your carry-on luggage which will be X-Rayed. If the security staff wish to do a physical check then be prepared to demonstrate it working.
The altitude limit set by Apple does not apply to aircraft.
The cabins are pressurised for the comfort/survival of the passengers and so the iPod will work quite happily at 40,000ft inside an aircraft. For your safety and the safety of fellow passengers please follow instructions of the cabin crew with regard to use of electronic equipment during take off and landing..