Hmm... Not sure if the frequent HOME Menu accesses while ACNL is running are the root of the saved data corruption. It doesn't even matter if your copy is physical or digital.
The thing is, it's extremely difficult to accurately pinpoint what actually causes the data to corrupt. The game itself is so poorly coded that the corrupting can randomly occurs at any given moment, as a sizeable amount of reports over the Internet suggested. It seems like that some 3DS systems are more prone of that problem than the others, as my experience with my vanilla JPN 3DS evidenced a lot. It crashed enough times to tell that my old 3DS is kinda defective (other games on it worked flawlessly). I've performed a System Transfer to my newer 3DS LL, and the game never crashed afterwards, regardless on how long I play in a single sitting.