For some, collecting amiibo is a passion; a lifestyle. For the serious collector, removing the amiibo from its box is seen as an assault on its value, so there's a conflict of interests. On one hand, the amiibo is meant to be scanned and used in various games; that's why they were made. On the other hand, collectors want to leave them in the box because I have no effing idea why. Maybe they'll be really valuable one day? At any rate, Yacht Club Games heard you guys loud and clear.
“We got a lot of feedback from fans before release who wanted to be able to scan the amiibo inside the packaging so they could still use the figure [in-game] while keeping it as a collector's item,” David D'Angelo told Polygon. “We didn't see much issue with their request: while you can stand with a 3DS in store and try to scan it — we didn't think that was actually something people would do due to the nature of the content we were making. We do not plan to change how the amiibo is manufactured.” So when Yacht Club Games produced its Shovel Knight amiibo – under license from Nintendo – it didn't include the typical NFC “blocking plate” that prevents people from scanning the figure in the package. Usually Nintendo is pretty strict about this kind of thing, but it seems they conceded in this instance.