Thanks,
In regards to the CIA, are there any compatibility differences at all between that and .3dz?
And if I'm not mistaken CIA don't need headers?
As for the headers being unique, would there be any problem if I backed up the headers for a single game and used the same headers for a bunch of different games?
CIA don't need/use headers. That's why it's easier when wanting to play online. There aren't any incompatibilities either as far as I remember.
What people usually say is that having two persons online using the same header would like give an easy target to Nintendo. Using the same header for all your roms isn't that bad since you'll only be using one at a time.
But in any case, this is all theory. No bans have been reported and Nintendo hasn't shown any signs of wanting to do anything about it (yet). But piracy isn't supposed to be risk free either. In this case, it could be much worse than what actually is.