The issue you have not considered is usage and the cause of hard drive failures. For a desk top system the actual quality of the hard drive is the most important factor and components wearing out from long use is what you are dealing with.
With the iPod the biggest single cause of hard drive failure is physical mistreatment - people drop their iPods especially when running, drop them into water whether the pool or a wash basin, and otherwise damage the components including the hard drives. In this case even if the hard drive would be likely to last many years safely sitting on a desk, even the best hard drives will fail catastrophically and prematurely.
While it is true that the nano does not suffer so much from dropping, theft is still an issue.
It is the nature of the way iPods are taken every where with you that increases the risks of both damage and theft.
So while by all means use the iPod to transfer files from place to place, or to store them, never ever consider this as the safest place to keep them - it is not. Back ups and storage should be on external hard drives sitting safely on your desk or in another safe location, and the iPod used for the enjoyment of music, books, videos and podcasts on the move, and the transfer of files. Never for long term storage.