Only one time a day.
Seems that changing console date in settings (-1 day scan amiibo +1 day scan amiibo -1 day scan...) lets you bypass the limit but you have to close and reload the game every time.
For now i use it once a day.
The exception is wolf Link. You can rescan that when the wolf "returns to his own world" or whatever and bring him back. No one day limit. I don't know if it works when he dies. I would assume not but he's never died on me yet, just left when he couldn't follow me paragliding and stuff.