According to the Japanese version of the Nintendo website, the game supports amiibo, but most likely without a new line of figures. This means that new models of characters or ships are not to be expected.
However, old amiibo will get a second life. They can be used in the game to get bonuses, unique backgrounds, and rare emblems for multiplayer.
It is also reported that scanning figures affects gameplay. For example, Fox will be able to summon James McCloud for one mission a day, Falco will get a weapon upgrade, and Wolf will unlock access to his ship.
Overall, Nintendo is focusing on supporting already released figures, allowing old collections to be useful again in new games.