Yes, magnetic fields can affect your iPod's hard drive. It doesn't matter what the source of the magnetism is. Electromagnets or permanent magnets can do equal amounts of damage. What is important is the field strength of the magnet and the distance from your iPod.
Since no one outside a lab has the equipment to measure the field strength (and I've not seen posted on Apple's site what field strength numbers might affect the iPod), you're best bet is to keep speakers, fridge magnets and the like as far away from your iPod as feasible.
You should know that the field strength drops off quickly with increasing distance. Its proportional to the inverse square of the distance. So moving your iPod an additional small distance further away from your speakers will make a significant difference.
If you have a particular spot near your subwoofer that you just have to have your iPod sitting at, you could shield your subwoofer. Go get some sheet steel (cheap rusty carbon steel works best for this, don't use stainless) and bend it into a box around your subwoofer. Use screws to connect any cut pieces, i.e. guarantee electrical contact between the pieces. Run a wire to ground from the box and you'll complete the shield.
OTOH, if you're unlucky and you guessed wrong on distance from a magnet, i.e. iPod's HD is adversely affected, don't worry too much. Hook it up to your computer, reformat the drive and reinstall the iPod OS and all your tunes. It will work once again.