On the 3DS savegames are stored much like on the DS, that is on an EEPROM in the gamecart. On the DS these savegames were stored in plaintext but on the 3DS a layer of encryption was added. This is highly likely a streamcipher, as the contents of several savegames exhibit the odd behaviour that xor-ing certain parts of the savegame together will result in the plaintext appearing.
The reason this works is because the streamcipher used has a period of 512 bytes. That is to say, it will repeat the same keystream after 512 bytes. The way you encrypt with a streamcipher is you XOR your data with the keystream as it is produced. Unfortunately, if your streamcipher repeats and you are encrypting a known plaintext (in our case, zeroes) you are basically giving away your valuable keystream.