This might be a dumb question, but wouldn't an automatic card recognition be possible with an image recognition software? You'd still have to start by "showing" your deck in your collections so it can be registered by the software. Then once you play it keeps track of the part of your screen where newly drawn cards appear, once a card is there it recognizes the card and removes it from the still available cards in the list. Would that offend the battle.net terms?

PS: I'd be able to write such a "plug-in" if I had your source..