I take my amiibos out of the box except for one or two that I think I bought twice by mistake. I like to use them so they do me no good in the box but they do look cool if you have a collection all in boxes.
I only have two Amiibos (Pearl and Marina), but they're both out of the box since I wanted to scan them into Splat3! If I was displaying them, I'd rather keep them in their box, but I definitely want any in-game perks that they have, since I think it makes it more fun!
Most Amiibo I’ve taken out of the box so I can actually use them, I have no interest in keeping any specifically in their boxes for collectible reasons etc. There are a few I’ve left in the boxes.. but they’re only Animal Crossing ones, because I got them when they were kinda useless during the Wii U area, and haven’t felt the desire to open them even for The Roost in NH.
Boxes take up too much space. 7 out of 8 amiibos in my house are displayed neatly in one place as a Splatoon family and Tom Nook is standing on a shelf in another room with some other figurines.
I don't have room for packaging so out of boxes they go. I only have my favorites, and since they're relatively cheap figures, I don't baby them like I would something more expensive.
I have mostly animal crossing amiibos, Kirby, Meta knight from smash, flying Meta knight, Dedede, Wolf Link, Marina, Pearl, Callie and Marie and a treasure goblin from diablo. All out of the box, I only have one I keep in its box, it's a big detective Pikachu, I like the box because I can set more Pikachus on top of it for display.
I don't have any anymore, but when I did I always unpackaged them. Leaving them in the box seems kind of..... eh. Unless I happened to be the most extravagant collector ever for some bizarre reason and had one of every kind in existence. I wouldn't bother otherwise.
EDIT: I need to clarify, however, that I'm only talking about my personal preference here. I would never judge anyone else for keeping them in boxes. If it makes you happy then go for it! I mainly just meant that I wouldn't ever do that myself unless I had a collection of every last one.
I have Animal Crossing and Zelda (Botw/TotK) amiibos, but I keep them in their boxes; Not necessarily for higher resell value since I'm most likely going to keep my amiibos, but I never really needed to use them. I think they look great in and out of the packaging, though. ^.^
My brother has Smash Bros. and Metroid amiibos, but he also kept them in their boxes for the same reasons. They're displayed in the living room on our collectible shelf.