Actually, if you use Gateway Ultra 3.0 on a 6.x+ sysnand (this applies to emunand too. If sysnand meets those requirements, then saves use new encryption regardless of whether or not you're in emunand),
Classic Mode WILL use the new encryption! It doesn't matter if your in emunand or not!
It's only Gateway mode that doesn't use it yet. Of coarse being on 5.0 or lower sysnand firmware means Classic Mode uses the old save keys like usual.
Not sure if it's even possible, but if you have 4.5 emunand on a system running 6+ sysnand, then save encryption may or may not use the old keys. But I honestly know of no one who tried to boot an emunand that's older then the sysnand.
Not sure how Gateway's save dumper works or if it decrypts the save on export like SaveDataFiler does. But as of right now, it can't dump Card2 saves. I haven't tested it, but it might not be able to dump any save using the new encryption. But that's assuming it was supposed to decrypt the save for you. If not, then only Card2 saves are not supported yet. (although you can just dump the entire rom instead and use it in Gateway mode. Card2 games can have their saves extracted with SaveDataFiler, if the save doesn't use the new encryption! Just have the rom selected in the Gateway multirom menu before starting SaveDataFiler)