My father and I stapled hundreds and hundreds of roofs over the years with no rusting issues, mostly asphalt shingles though. He stapled for over 20 years 6 days a week. The staples bite down into the wood which makes them hold very very well. A nail driven with an air gun would make me think the shake would split too easily.
The two things you still see stapled down these days are wood shakes and sheathing. Can't recall the last framer on new construction use nails to lay the roof decking.
I've had less problems with stapled roofs over a 7 year period than 3 years of nailing. Figuring 40-60 roofs a year over the time frame makes me wonder which method is better.
Now all the roofers I know all nail with either Hitachi, Paslode, or Bostitch guns.