It could even be like how Nintendo is doing the Game Boy last year, with basic Game Boy on the standard plan and GBA with the Expansion pack. Basic DS games would be on the general Online plan, and newer 2DS/3DS games with the Expansion Pack.
Unless they prove me wrong and we finally get Mother 3.
For example, a switch port of Link Between Worlds is more valuable if you can’t easily buy a used 3DS and pirate it.
But it is probably just Nintendo being protective of their IP and means nothing.
Could see the final year or two of the Switch having a bunch of them tbh, similar to some of the bizarre late period 3DS ports (e.g. Bowser's Inside Story)
Thing is though, nothing will be as pleasant as using it on the actual hardware. If it isn't on an actual DS/3DS, I don't see the point in playing at all personally unless they radically change the controls to a rereleased game.
Which coincidentally was also how I modded my WiiU: https://github.com/smealum/haxchi