^Basically that. Yes amiibos are popular but just like most "popular" items, it's only selling b/c it's popular and rare. You take that away and people are no longer interested. Yes you'll have those people that just love collecting them but others will see no need to anymore.
This happened with Beenie Babies, rare LEGO's, Simpsons toys, etc. Whenever a company decides to actually stock the product, people lose interest. It's a basic business practice to limit certain items knowing it will drive sales of other items.
Nintendo is just underproducing them because they are a bunch of cheap assholes. It's no secret that they are frugal in their manufacturing of products whether we are talking games, accessories or specialty software like these amiibos. They're terrified in this case they will make too much and be stuck with them so they go the cautious (and cheap) route of minimal production to ensure they'll never be over. But ultimately it's just because they're cheap...always have been with everything they've made.