I'm not much in favour of unnecessary visual gimmicks in dominion online -- I think the game attractive and fun enough in itself to do great without much embellishment.
However, I think that an (optional) animation poping up at the moments when cards are being shuffled would be both cool-looking and pretty useful. Sure, every seasoned player is much used to following the log. Sure, the deck has a number showing the number of cards left before the next re-shuffle. And yet, I'd be very happy to have this added (and fun!) visual marker of the important point in deck rotation that the shuffle is.
I also think that a card-shuffling animation could tie in more the online game with its physical equivalent, and it could help the novice player grasp the basic idea of the decks' mechanics quicker.