Quite different.
Amiibo cards are collectible items as well.
I love collecting them, for one. So it's not the same.
When someone is selling in-game villagers, they're essentially selling you code and keeping all the money for an "item" they don't own the rights to for themselves.
With the hand-made amiibo cards, it's kind of like selling pirated DVD's/CD's. While I know that some people personalize them, add their own unique art, etc., if you were to burn your own DVD copies and then add unique packaging to them and sell them at a profit, do you think that would make it okay?
While I have definitely downloaded movies and songs off of the Internet, I would have never thought of selling them.
I have shared them with friends - sure - but making money?
I mean I don't want to judge too harshly but if you're aware of piracy laws then you probably know the answer.
I know people also make custom plushies/sculptures/paintings, etc. and this is where it gets a bit tricky for me. Because, potentially, Nintendo could also step in and say that this is wrong. I think because they're such a big and prosperous company with some of the most recognizable and iconic video game characters (Mario) the lines get a bit blurred here.
But imagine if people started selling art of some Indie game characters at a profit - I could imagine some of the game devs not being too happy.