Definitely sounds fun!
I don't like the idea of "really huge decks". There needs to be a reason for a huge deck, and it seems like the reason should be more important than the huge deck itself. You can do it, but I don't see the point - making the deck huge just makes it harder to keep track of, and you don't want to throw in complexity just for the sake of complexity.
I do like the idea of cards being able to modify cards, or modify where cards appear in a shuffle, or stuff like that. That's a strategy space which basically can't be explored in physical cards. You can make your deck be more than just the set of cards that comprise it - maybe you can "glue" two cards together so they always appear in order, or stuff like that. Maybe make your terminals 'repel' each other! We've all wanted that...