I think you are better off formatting them the old fashioned way. We have something similar at work and it doesn't work on hard drives. The magnet is not strong enough to penetrate the shell of the metallic hard drive. Tapes, no problems.
There's something call the Hard Drive Duplicators, a device you can clone hard drives, 2 or more at he same time. Here's one, http://tinyurl.com/odsoz. I think some do erasure, too. But, these are usually expensive and useful primarily for industry/business. A PC is sufficient for most cases.
You can also try using strong magnets, say, the one in junk yards which can pickup cars. Just take all your hdds and stick them onto one of these things, voila, they're all clean. LOL Kidding only.