I have a flash modded 5th gen classic and I've seen people talk about magnets hurting their hard drive, but will it affect the other components?
#Do magnets hurt iPods?
royal viper
pine hinge
It does not. Original iPod hard drives are susceptible to high-strength magnets because it can erase the data on the spinning platters, but flash-modded iPods will have no such problem. Nothing else in the iPod is sensitive to magnetism. You will be fine!
tribal rune
HDDs can be influenced by many different means (especially the heads might have issues with reading the faint signals from the platter plus it can just drag the heads assembly around), but it might be hard to do any damage through the iPods and HDD case. Still a big strong neodymium magnet can do some harm.
After converting to flash memory - if you use too big (talking about really big magnets 1kg/2lbs and bigger) one it could cause internals to bend and short. But chances are small in real life conditions.