I actually have yet to personally have any issues with counterfeit games. I mean, I do my best to do some back ground checks (I mostly shop on amazon and a few other online shopping sites that require accounts and have return policies. I also don't shop on eBay, that place is a danger zone.) before I purchase a game. I do understand however that there are people who might not be as cautious when shopping for used games online.
I also will admit that I temporarily forgot that the old Gameboy /Advance games have internal batteries that run dry or corrupt (once again, I feel lucky knowing that my collection of game boy games including my copy of Yellow have not run into these issues), so I can definitely understand how having a safe outlet for playing older games such as the 3DS VC is definitely an attractive and sensible option.
I think it comes down to personal preferences in the end with both sides having its Pros and Cons. I might be a little more hardcore to go to the trouble to hunt down an old used copy of a game, but I personally take its pros and cons over the pros and cons of purchasing the game on the virtual console.
I enjoy physically owning games, and I enjoy collecting old games, and the VC doesn't really provide the same experience that I'm looking for when trying to acquire and replay older games.