Digital of course. Why would I want to carry around game cards for a portable gaming console?
The golden age of physical game collection is dead- at least when it comes to Nintendo games. ****ty, flimsy boxes with plastic-saving holes cut out of them, non-reversible box art, and a four-page instruction booklet is hardly a collector's ideal purchase. Not to mention the mere existence of a digital version significantly reduces the long-term value of a physical game card.
I know Nintendo's eShop purchase system is broken in comparison to Steam, XBL, and PSN, but a physical game card is no more safe from theft or damage than your 3DS console is.