The eMMC (why does everyone call it a NAND ? Well, I guess it does use one anyway) is encrypted using a per 3DS key set by the bootrom to an AES hardware keyslot, these keyslots are write only and cannot be read.
Therefore the only way to decrypt the content of an eMMC chip is to use the AES hardware engine of the 3DS it came from. The whole process is rather slow and can only be done if you are running your own ARM9 code on the device (aka kernel mode).
Also, just to be sure we are on the same page here, you obviously can't write back the decrypted content to the eMMC pages, it needs to be encrypted with the right key.
You get the idea.