I'm very confused on all of these posts saying they trust the physical copies more.
What does trust have to do with a virtual or physical copy of the same exact thing?
regardless of if it's a hard copy or a downloaded one, it's still the same thing to the 3DS. The only difference is that the virtual one is all saved onto your 3DS/SD card instead of on the game cart.
If it's a matter of trust in regard of potential problems, I'd think that the physical copy would be worse. You could lose it, it could break/stop working. To me a downloaded one would be better because you can't lose it and the only way it can break is if you break your whole 3DS.