Do you think, we can ever sign a save and send it back to game?
If somebody ever successfully retrieves the bootROM and sees how the 3DS tells the system how to generate the AES MAC and then releases it, then anybody could do it with software. While that sounds simple on paper, it is actually a very big undertaking that requires specialized equipment to do properly. There is a blog of somebody who seems to be seriously undertaking this process and has taken the first steps starting chip decapping. (
http://gaasedelen.blogspot.com) However, there is still a long way to go and there have been no new updates since late March.
The second route would be if there are any vulnerabilities that can be exploited that have been found by those who have dumped the RAM of the game such as Bond697. He has stopped by a few times and provided updates and there seems to be some good things on that horizon, but even he has cautioned that there is no timeline on any rollout.
Lastly, if both of the above methods fail, there is always the way that Datel is most likely doing it. This is done (most likely) by using a hardware modded 3DS and custom made software that actually is highjacking the portion of the system that signs the saves. You can picture it by using the philosophy of, "If I can't crack Nintendo's signature system, then I will just use it to do my dirty work." However, this would be limited only to a smaller group of players who has the technical knowhow to mod the system and the software engineering knowhow to create the programming necessary to force the system to do it. It has been done (most likely) by Datel who obviously isn't going to give away it's money making secrets.
Long story short, just like anything, there will probably be a way to do it in the future. The system is designed by humans after all and there are always going to be imperfections in the security of the system that can be exploited (like the firmware 4.x exploit for flashcarts.) With that being said, Nintendo has drastically stepped up it's game compared to previous systems and is making it so that it's not a walk in the park to get at. It is a strategy employed by countless entities in the past. Design a system eliminating the most conventional attack routes. This will discourage a group of potential pirates (because this is the main reason why security has been upped) since it isn't simple to crack. Then you make further improvements that will cost those who are still interested in cracking it (more well funded pirate groups, enthusiastic player communities such as the one that exist for Pokemon, programmers who like a challenge, etc) lots of time and treasure to do it. The hope would be that you delay it to the point that by the time they fully crack the system, you are already about to roll out your next gen system which then renders your loses to pirating much lower than past generations.