Conspiracy theory: if they can detect who is using a hacked pokérom, then they can tell who is using a copied rom. Crackdown before the end of the year!
Well, currently, WFC works great with any ROMs. If you have actual carts, then you shouldn't have any issue since there are some great backup programs that have come out recently. So your backups can truly be backups. Of course, you'll need a slot-2 device as well.