"Nefarious plot" is probably the wrong term here. What I really mean is "clusterfuck of bullshit." You're assuming they actually could predict demand and as such artificially limited supply to increase demand even more. It doesn't work like that, especially when you consider that the only region where the goods were incredibly limited was North America, in no small part due to the port issues.
Animal Crossing as a game is popular, sure. But nobody remembers your goddamn player character because he's the most unremarkable blob of whatever in the game. They remember the characters you interact with. A Tom Nook amiibo would fare much better than the Villager because, again, the Villager is intentionally unremarkable. You could say the same thing about Robin in Fire Emblem but Robin has a pre-defined personality and the only real decision you make for him/her is regarding marriage.
They signed the contract BEFORE THE STUFF WAS EVEN IN PRODUCTION YOU IDIOT. This was pretty much stated earlier with the store exclusive figures of wave 3. They didn't know how popular they would be and months before the first wave even hit shelves these things were in production. Golden Mario was probably a similar case.
Nintendo isn't aware of this, they thought to produce enough characters to meet the demand relative to that character's popularity. They accounted for that, not for the diehard collectors who need to buy every last one of the fuckers. Now they're accounting for those people too and are upping their supplies to hopefully meet demand in North America.
And yes, I do think I understand the retail toy industry better than Nintendo because this is one of their first significant outings in making toys like this when before they've just dabbled in the occasional figure and maybe a plush of Pokemon here and there, and those things are constantly produced to satisfy demand. They have much less of a grip on it than, say, Hasbro, who has been doing this for some time, and usually make it incredibly easy to find anything that they produce within the run of the product. You never see Transformers go out of stock for months unless they've said "we're not making any more of these particular characters on X date."