If you download a game from eShop, it will act exactly like a game installed as CIA. The save only gets created when playing the game so how you get the game isn't important. Only where you play it is what's important. In this case, at least for now, any save created in GW Mode will use the old encryption. Classic Mode uses the sysnand encryption keys so it will depend on the firmware of your sysnand. It's like that since update 3.0 because before it also used the old keys (which rendered retail cards' saves created in firmware above 6.x incompatible). That's probably why GW's team changed how Classic Mode works.