It sounds like a lot of people think you can't re-download digital games, but I know at least one person who has successfully transferred their account to a new 3DS and was able to re-download their games. It's a hassle for sure, but possible.
I'd go digital, because I already own a large number of 3DS carts that have never been played. If they were downloaded and I could switch between them more easily, I'm sure I would get to play them all. There's a part of me that knows the physical carts will hold collector's value one day (I actually have two copies of Shin Megami Tensei IV, one still sealed in the collector's edition box), but considering the mileage I expect to put into Smash I'd rather just have it with me at all times.