It's much better to have a hot item restricted by supply than it is to over produce and sit on on launch units for the entire lifetime of the product like the Wii U. And the 3DS stock issues are because its a portable that only sold 60~ million units and is on the last leg of its life while Nintendo shifts the product line towards cheaper 2DS units.
The thing I think a lot of people don't understand is how you don't want to over produce items and unless you're selling iPhones its impossible to accurately gauge demand for a product. Nintendo is being smart here, they still managed to ship a large amount of Switch units and are now working to catch up to demand.