I hardly ever use my DS so I don't know much about the R4 and stuff, but I really don't see how this feature will help combat piracy.
The people who want to download games for free will still get an R4 or whatever they'll make for the 3DS and pirate whatever they want. All this feature will do (assuming there won't be some kind of special protection, which I find hard to believe), is make it extremely easy, and thus more attractive, for people who normally wouldn't buy an R4 to still pirate games. Sure, it's on a smaller scale than the 'real' pirates, but it's still an increase in illegal activity.
And it gets worse. I've frequently made a point that most pirated games aren't lost sales. Yes, pirates selfishly want to play games without paying for them, but that just means that they're far less inclined to buy games if they can't get them for free - they'll just get something else. This new group of pirates would be a group that isn't that much into the whole piracy thing from the get-go, so it's a lot more likely that the games they pirate are lost sales - if they didn't get them for free, they might've bought them.
I certainly see the (legal) use for features like this. I think it's comparable to what I do for most PC games: I visit pirate sites and download no-cd cracks just so I don't have to swap disks whenever I want to play a different game. The same would apply to copying games to the 3DS' internal drive. It's simply a matter of convenience. It's just that I wouldn't like to see Nintendo shoot themselves in the foot by facilitating would-be pirates like that.