On my 5.5G I can definitely hear some soft but distinct noises, including:
(1) Disk spinup/spindown
(2) Disk seeking ( a soft clicking-like sound)
(3) Disk platter gyroscope effect (if you rotate/turn the iPod while the disk is spinning you can hear motor noises of the disk counteracting gyroscopic effects of rotational inertia)
#1 and #2 are normal to any disk's operation and are not killing your iPod. Apple firmware does the same but they seem to access the disk a lot less during normal operation (likely simple UI + itunesDB?)
#3.... well that makes me cringe a bit more. I'd expect Apple to choose a HD that's designed to take that, since if you're jogging and the disk spins up this is bound to happen. It definitely sounds awful and turns your soul cold when you hear it, and I've seen desktop hard drives in external enclosures been trashed or at least partially damaged from sudden rotation (rough handling, fall onto its side, etc)
Basically I wouldn't worry about it
