So from what we know, if you have a Gateway you should be using .cia files. There's really no reason not to. I know some saves won't transfer over which sucks. But I'm pretty sure that Pokemon, Animal Crossing, and other card2 games can be transferred. It's really not worth the risk to use .3dz files. Especially if they're banning public and private headers.
There's already a known workaround for Card1 saves to work with SaveDataFiler.
Just rename the save file to 000400000FF40A00.sav (seems to be SaveDataFiler's ID, so that save data will be loaded when you run it).