You can also get Nookington’s by having someone enter your town locally, so you’d need two copies of the game and two 3DSes/DSes. I’m not really good with wiimiifi so you should ask someone else if you have this question, but as far as I know, this is the only other way besides local play that you can have someone visit.
I think you were using either the Wii U version or a version of the game that had a glitch that did this, because this doesn’t normally happen. Unless you mean upgrading from Nook’s Cranny to Nook ‘n Go.