A little of A and B. If you somehow made a cart that had the same encrypted contents of Mask ROM and interface logic to the DS slot, then yes, it would work. This is however not what people normally mean. They don't want just pirated copies from some Asian knockoff plant, but to be able to run whatever code they want. Ironically, the methods (signing) that companies like Nintendo and Sony use mostly prevent home brew (at least in theory). For now, their methods on the PSP Vita and 3DS are preventing both home brew and casual (noncommercial) copying. I doubt they'll prevent piracy of actual Nintendo cartridges simply because there are IC factories in a ton of countries that can illegally make Mask ROMs and copy the unique Nintendo interface logic. Pirates win, home brewers don't. :/
You will likely not be seeing Vita exploits for a long time due to lessons learned by Sony and the fact that no one wants to tell Sony their only exploit - they'll wait until #2 like I said above!
After reading this, I had this thought of using an actual 3ds game as your "signature" and have some wires that comes out of the game to connect onto something, then run the code off of there.
you know this is a good idea , but it depends on if it perform constant hash checks in the code, ,its funny cause i just was watching a video where this same type of method is used, it was an angry nintendo nerd video on you tube,he was reviewing bible games for the NES , and there was a company that made shatty bible games and they were the only company to make games for the nes that did not have a liscence from nintendo , so one of their games was a sort of pass through cart where you plug the game into the nes cart slot and then it has a cart slot on the back of the game cart for a real liscenced nes cart to piggy back on top of it ,to get around the game not being an official nintendo liscenced title ,though im sure security on the nes was nothing like the 3ds