Whose to say they hardmodded them at all. They could be using 4.5 consoles with code running to make the 3DS sign the saves in software. Smealum seems to have indicated he has already figured out how to decrypt 3DS roms which appears to have been something he's done through software. (he won't disclose how he does it though, but I'm sure it's not a hardware mod)
The 3DS's may have custom homebrew coded in house by Datel/Cyber that does this encryption/decryption stuff and additional homebrew that connects them via wifi to a server they control so that they can then proceed to send other folks saves files into a que line for the 3DSs to process. That's my theory on how it works. Which in the end makes Nintendo's attempt to keep out hackers via hardware a moot point if your software isn't secure.