the files might both be for nintendo video (for example), however the system puts a 'lock' on the file so only that one system can open it with the 'key'. Two files might have the same content but be locked each for a different system's use.
The hardware in your system is uniquely identifiable, it uses that
the 1's and 0's of the file would have to be different for the file to know which unique hardware to run on
therefore when compared the files should come up as different
so if you can find files that are EXACTLY the same on 2 different 3DS consoles
i think its much more likely that we can edit that file and exploit it rather then an obviously encrypted one