*puts on nerd glasses*.
Currents are only induced when there is relative motion between current carrying conductors. A magnet touching "shielding" paint will not cause any issues at all. So, your concern of ground loops is unfounded. The only way to create a ground loop is if you used the shielding paint as the ground.
Instead, the shielding paint acts as a sort of faraday cage, blocking out external magnetic or static interference. It does not act on the circuit itself.
In reality you are better off shielding the wires, as that will produce a true faraday cage, whereas the paint will not properly disperse any external interference. (i.e. only working in one direction).
Now, to answer your side question, if you attached your ground wires to the paint itself 1) that wouldn't be very reliable, I wouldn't think, and 2) that would play more of a part in ground looping. Everything still must go to the ground wire on the input jack. So you'd be attaching grounds to the paint, and the from the paint the jack. That doesn't make a whole bunch of sense to me.