The narrative has since mutated to "why can't they be like Apple?!1"
Not many companies has mastered economies of scale, logistics, and just in time manufacturing process the same way Apple has done, and even they have supply problems if a product gets too popular. Also, they didn't come off their worst selling hardware ever.
It's really apples and oranges (pun kind of intended), but it should be flattering people are even putting Nintendo anywhere near close to the best logistics company in the world.
They did, but they were completely caught off guard at the magnitude at which it took off.
I'm honestly surprised myself; March isn't exactly the time for people to drop hundreds of dollars into a shiny new tech toy, Zelda is really far from the "Wii Sports" type of game that has universal appeal, and at launch there wasn't anything other than 1-2-Switch (which afaik didn't set the world on fire). But they caught lightning in a bottle once again, and it looks like they're taking every measure possible to not leave money on the table. The last restock lasted several hours and it seems like they injected an enormous stock.
I bet even now, Nintendo is probably taken aback at Mario Kart 8 sales an it's halo effect on Zelda and Switch sales. They probably planned Mario Kart 8 to be a stopgap measure before Splatoon 2 came out, not to be another cultural phenom in its own right.