I'm not so sure about that, while I'm sure it would be possible, remember the 3DS is to boast highly "advanced" anti-piracy technology, so it might be nearly impossible to hack in a fake Pokemon onto a cartridge. Outside of what hacking can already do for the games.
And while I would be okay with downloadable Pokemon, I don't know about it. To me it sounds too complicated to deal with.
Anti Piracy =/= hack proof. As long as hackers can get to the save file, they can hack Pokemon. Signing the files would only slow down the hackers, as they would find ways to hack them like on the 360. In fact, most 360 hacks have to do with hacking save files, just like with Pokemon.
They might be able to block out memory edits (action replay) with the 3ds though, but don't count on it.
The only way to really stop hackers is to start banning people from online, like with xbox live. If nintendo cares about online this gen, they will learn from what happened to PSN and start banning people.