Most of them have a rule either or two or three layers and they have to pull the shingles, otherwise it is fine.  My guess is with 2 or 3 layers the screws won't be long enough to actually bite into the wood.  I've done both I like the extra sound deadening and even insulation of the shingles under the steel.  As long as the roof isn't leaking and the layer isn't too thick I have no problem with it.