If you place the magnet close to the hard drive or a floppy disc, yes it will erase it, and possibly damage it. I would place it as far away from the sub as possible to keep it from getting jarred from vibration.
The power of a magnetic field depriciates as a function of 1 / r^2. Even if you were to rub your hard drive against the magnent on the sub, it is very unlikely it would damage anything (floppy disks are a different story because they are far thinner). Unless you plan on mounting your hard drive to the sub's magnent, your safe.
I know people on this forum before have mounted their computers inside sub boxes, and as far as I know, they havn't had any problems. You should be fine.
Couple 80mm or 120mm fan's definitely won't hurt. Damage due to vibrations are probably the worst offender for killing HDD's in CarPC's. (Short of getting into a high-speed accident while changing MP3 playlists).