I got hold of a bunch of the AR cards you can scan in the Pokedex 3DS app (don't worry, I'm gonna add them to the site soon!)
When I scan them, however, not all the Pokemon register. Mostly it says "Unknown card" but it has the silhouette of the Pokemon and the card is registered in the sticker book, but not the Pokemon. Only Victini, Cobalion, Terrakion, Virizion, Reshiram and Zekrom were the new ones unlocked.
So is there a limit per day or week or whatever?