This is probably the case.
Weirdly, online stores seem to be differing from in-store items. As a couple of examples, if I ordered my Gamecube controller from Amazon or even the official UK nintendo store, I wouldn't have gotten it until well after the game's launch here (I guess it also didn't help that my copy of the game with the adapter failed to arrive on the promised date, but I digress). In contrast, I went into my nearest game store, and by coincidence, they had the controller, several in fact. The wall behind the counter of the GAME i entered was dominated by Amiibos too.
With the Marth Amiibo, the store I work at has one, and checking the stock of stores everywhere nearby suggested that they had one, but ordering the few in stock in online retailers wouldn't deliver the thing until January.
The Adapter for the gamecube controller is an online exclusive for the most part, so acquiring one, even by itself has to be done over the net, and it seems that the majority of Nintendo products are bought over the net as of late to the stock was indeed low. Besides, why would Nintendo keep selling the gamecube controller, but stop the adapter that you need to even use it in the first place?