I agree that we should be able to unlock hidden Amiibo content like normal DLC for those who doesn't want to be over encumbered with dozens and dozens of figurines.
But, I'm also happy to see that Nintendo is interested in cooperating with indie developers to create special products like this. If Playtonic make a Yooka-Laylee Amiibo in the future, I hope the content it unlocks is not something as important as Coop mode like Shovel Knight. Maybe an alternate costume for Yooka, or different colours, something that doesn't change the gameplay and the experience too much.
Alternatively, I would personally prefer a non-Amiibo, higher quality figurine of Yooka and Laylee (like, say, a Nendoroid/"figma" figure) instead of a cheap Amiibo with unwanted DLC-like functionality.