The Banzhof/Akron book says that the reason they put the two extra Magus cards in the deck was because when the guy who supervised the reproduction of them in the '80's checked the gallery where the original paintings are held, he found 80 paintings rather than 78, and decided to add the extra ones to the deck.
They also mention a confusing (to me) theory about how there should really be 24 Majors, and thus the two extra cards are extremely important.
I'm beginning to think that Crowley never intended to expand the deck, but I like leaving them in and trying to figure out how their meanings differ. Never has more than one shown up in any reading I've done.
Oh, and Emily - the eight-armed Magus is NOT the usual one. If you get the deck with only one Magus, it's the Mercury Juggler one.