I'm fairly confident you're incorrect. There's a single shared account between the 3DS and Wii U online stores, and I also know for sure that 3DS purchases are tied to your user account, rather than your hardware. I suppose it's possible that it works differently for the Wii U than the 3DS ecosystems, but that seems unlikely. You can still only have an account attached to a single console (of each type) at a time, but if you lose one or it dies, you can reattach your account to the new one.
Sorry, but that's the way it is. You do share the 3DS and Wii U accounts, but game titles are tied to the console. Nintendo has no instructions on how to transfer games to a different 3ds system without having both of them physically there and working [0]. I wanted to trade in my 3DS for a discount on a "New 3DS", but wouldn't have both systems to transfer my games. (Though I've read most Gamestop's will let you do the transfer in their store when you do the trade-in, I haven't tried).
It seems a Kotaku author was able to get their games transferred by contacting Nintendo directly. So at least there's that [1]. There's no direct way to download your games onto a new 3ds. And additional source about transferring between systems [2].
they are not.
you only need to contact Nintendo if your account is still TIED TO ANOTHER 3DS.
However if it isn't you can just buy a new 3DS and selling the old one before you have the new one. If you've forgotten to detach your account your games are missing.
Here a german letter (I translated it) that I got from Nintendo before selling my 3DS (I wanted to sell the Games with the Account):
Die Spiele, die Sie mit Ihrer NNID erworben haben, werden für den Nachbesitzer also nicht verfügbar sein, vielmehr sind die Lizenzen der Spiele
mit Ihrer NNID verknüpft.
Spiele sind auch nicht zwischen NNID's übertragbar.
Eventuell vorinstallierte Spiele (wie z.B. Mario Kart 7) sind mit der Seriennummer der Konsole verknüpft und werden für den Nachbesitzer wieder
verfügbar sein, solange Sie vorher keinen Datentransfer auf eine andere Konsole aus der New Nintendo 3DS-Familie durchgeführt haben.
NNID = Nintendo ID.
In short it says Licenses are connected with the Nintendo ID. Only Games that are pre-installed on the Console will be tied with the Console ID, if you didn't do any Datatransfer to another Device.
However I detached the ID and bough a 2DS later and I still can play all the Games on my NNID. Basically I only sold the 3DS + Cartridge Games.
Calling Nintendo to transfer your account in the event an old system becomes inaccessible is inconvenient, but not insurmountably so. It's good enough for me to consider games not tied to the console.
Your account is tied to the hardware (1 3DS and 1 Wii U). You can move your account from one hardware to another if you have both on the same room, or with a phone call.
