I recall reading a couple of years back that, as part of Nintendo's new approach and desire to cut back on expenditure during the leaner 3DS and Wii U years, they deliberately seek to only manufacture items in a number that they can immediately sell without having a need for stock storage. This is why the launch of the amiibo range and the Classic Mini had such low volume available; if the demand is there then Nintendo will later make more.
It's a pain for consumers when something is popular but, from a business point of view, it makes sense. As long as people do then buy the items once they're re-available, of course!
Note: I'm not "defending" Nintendo on this; just describing how they do things.
EDIT: Just to show that I'm not making things up,
Iwata-san mentioned this during a Q&A session at Nintendo's "72nd AGM" in 2012:
Iwata wrote:..In fact, one of the challenges in the video game distribution industry in Japan is the higher inventory risk; it is a bigger challenge than ever before. Since it is common practice in this industry that retailers take the inventory risk, their profits from good sales can be easily wiped out by surplus stock. Therefore, when the sales pace of a game with a short lifespan is slower than expected, it is reasonable for retailers to reduce their prices. Previously, a retailer’s price cut was rather independent from others, but nowadays the information on a price markdown at one store is likely to affect other retailers in no time through the Internet, which results in a collapse of the market price. Consumers tend to see such a product as one with a bad reputation...