"It's not surprising that a hard drive based ipod might have trouble at altitude, the heads in them fly above the disk on a cushion of air, so the air density would affect the performance. Specs tell you to limit operation to < 10,000 feet. I've heard of hard drives failing in antarctica due to low humidity as well."
Hummm.... hard drives are environmentally sealed. Fluctuating environmental humidity and air density don't enter into the equation.
Perhaps dimensional changes to the housing due to lower pressures creates the problems?
Subzero temperatures will affect any lubricated bearing.
Any other WAGs?
Edit: I sit corrected: "The connection to the external environment and pressure occurs through a small hole in the enclosure (about 0.5 mm in diameter), usually with a carbon filter on the inside (the breather filter, see below). "
Found on Wiki, FWIW.