The only possible explanation I can think of is that a replacement product is in the works (e.g, wider game selection, SNES support, downloadable games, etc). Otherwise... WTF.
This isn't Nintendo's first super-popular product after all, at some point it boils down to them not caring enough to invest in their supply chain to keep enough stock on the shelves. Stores receiving five consoles at a time is a joke.
High prices, not being able to play some SNES games available for the Wii on the 3DS (wtf, just let play FFVI on the go), poor library (I know, licenses, but still), etc. make feel like they don't care.
I would be shocked if the Virtual Console wasn't running on the Switch by the end of the year.