I will stay with just one (physical) copy for now. I might get a second copy (digital) later if I do get a second 3DS; without being able to run both villages at the same time I see no reason for having the extra copy.
BTW, I saw somewhere that it's possible to have multiple villages on the Digital version. You basically have to swap the SD card for a fresh one (DON'T COPY THE FILES!) and download ACNL again on the empty card; by downloading a fresh copy, each copy is allowed to keep it's own save, allowing the player to just swap the SD card when he wants to change villages.
I didn't test this, obviously, and I only recommend others to try it if they don't fear losing their villages, given how picky ACNL usually is with making backups of it's save.
Edit: just saw a post on this forums stating that doing the above prevented a player from accessing one of his villages. Unfortunately I can't test it myself as I don't have a digital copy.