Can magnets harm an iPad?
You should be fine. As you note, there are magnets (which are actually fairly strong for their size) in the iPad and Smart Cover. There are no magnetic components aside from the Smart Cover attachment points and the unlock sensor—there's a magnetometer for the compass, but it doesn't use a magnet.

Furthermore, the whole magnets damaging hard drives thing is a bit of a myth. You can wipe them with magnets, but it takes a very powerful one, pretty much nothing you'd have in your home.