Looks like your Amiigo's will get more use than Super Smash Brothers. Well, one of them at least. The official Nintendo of America Twitter account has confirmed that the Link Amiibo figurine will be compatible in Hyrule Warriors. Unfortunately no other information has been confirmed at this time.
I'll be interested to see actually how this will work. We know that Amiibo's can be used in Super Smash Brothers to level up characters so your Amiibo will contain all of your stats for that character. You can level up your characters in Hyrule Warriors as well but there is no online play. There is local co-op so I am assuming that maybe this will be used when you have someone over or you go over a friends house to play. You can bring your Link Amiibo with you and will have all of your stats with you when you play with your friend.
It's also interesting that only Link will be usable when Zelda is also in that game and there is a Zelda Amiibo figurine. Hopefully in the future they will add support the Zelda Amiibo and hopefully they will release more Amiibo figures like Shiek, Midna and Impa for that game as well.