I have miiverse icon in Emunand. All changes I see only in emuNAND. If you see miiverse icon in classic, then, updating wasn't in emunand mode. You accidentally updated nand.
Of course you will have miiverse in emunand and classic soon as you boot into gateway you are in emunand, classic or whichever they both should have the GW3DS sign on settings. Did you not know that you can update emunand without updating your system nand?, I think you have your wires crossed a bit with the topic, others mean partially updating your system nand with miiverse icon, soon as you have that present in your system nand your 3DS cannot be used with gateway. Emunand it does not matter.