All you need to do with paper ballots is mark an identical number up the "right" way, and shred the real ones. Easy as pie.
With electronic voting, you need to be able to physically replace an encoded hard drive using an identical algorithm that was randomly generated - something that is not only difficult to do, but highly impractical.
You steal an election by magically finding a few extra paper ballots in a closet. You can't magically find a new hard drive that identically matches an existing one and switch it out on the fly.
They didn't use hard drives, but the physical act with Diebold machines took about a minute -- and that was before they found out they didn't need to pick the lock since it used a standard, easily available office furniture key.