great idea, i just installed the shelby pins, not sure about the look but it keeps my hood from shaking up at 75mph. i would have gone with your idea long before putting holes in my hood.
I don't imagine the field off of a 12 volt supply would be cause too much EMI. If in testing you found its field could affect any electronics, you'd simply put the pins in a metal housing; so it's not so big of an issue that can't be simply overcome.
Hood pins IMO although can be functional, are equally more for nostialic appearances. Now if you incorporate the magnetic system as part of an anti- theft device I think that might be more practicle.