There are no plans for Hyrule Warriors to make use of Amiibo, Nintendo has confirmed. Destructoid asked if the game will offer any such support and was told in response:
“Super Smash Bros. for Wii U will be the first game to support amiibo. Other games that will support amiibo include Mario Kart 8, Captain Toad: Treasure Tracker, Mario Party 10 and Yoshi’s Woolly World, with more to come.”
I can’t say this is too surprising! If Hyrule Warriors were to support Amiibo, we would have heard about it by now in all likelihood. Nintendo also previously stated before this recent comment that the figures would launch with Smash Bros.