I agree with the above posts. While the Amiibo thing is a little bit different - as creating demand for some Amiibo has thus created a demand for ALL future Amiibo, thus ensuring sales - there is practically no benefit for creating a scarce Zelda console. The system doesn't come with the game, it was just a way to move the system itself - and looking at sales, that isn't a problem, it never is. By creating a shortage of Zelda 3dsxl, they have only created interest in something, only to walk away from it. Honestly, the Amiibo thing I think is intentional, but I don't necessarily think the Zelda thing was.
For Skull Kid, Nintendo has done this before. With Skyward they released a limited edition with a gold wii mote. For Windwaker HD there was the gamestop exclusive ganondorf figure. Granted, neither sold out as fast as this, but Nintendo at least has a history for making a limited supply of physical extras.
For the 3DDS console, this is kind of surprising. Nintendo has produced Zelda consoles for pretty much every handheld since the GBA, as well as a Wii U console. Those sell well. But my guess is that they always over produce these items and eventually the demand dies down. Hell, I can still find Zelda Wii Us and the occasional Link Between Worlds 3ds at my local Walmart. Maybe those systems didn't sell as well as Nintendo thought. So I am hoping that Nintendo just grossly underestimated the selling potential. Because otherwise limiting a console at LAUNCH just to drive up demand for the other colors seems...risky.
There is also the possibility that had they not released the Skull Kid figure, this wouldn't have happened. That sold out so fast and caused such a stir that I wonder if scalpers just jumped on the console bandwagon and hoped the 3dsxl would be just as rare, thus creating a scarcity out of hopes of there being one (if that makes sense)