Ah that makes sense. But still, you would hope Nintendo would have some good internal archives, certainly from N64-era onwards.
That said, if all this source code and shit was required by iQue the company to get work going on their partner projects with Nintendo, it kinda makes sense Nintendo would upload it to some iQue specific FTP server and just let them have at it. Then when iQue's contacts at Nintendo left or were moved to other departments, knowledge of the FTP server (or whatever it was) also got lost.
I can see it.
There is also a version of the story saying it was the company that helped develop the Wii:
The source of the information is apparently a data breach from BroadOn, a company Nintendo worked with on developing the Wii itself.
In any case, it seems like someone made copies of specific things stored on the 'real' Nintendo vault archive server to use for their own work.
Archiving is one thing but keep stuff like this organized is another. Maybe it's just listed as the N64 source code or whatever and everyone completely forgot the same repository contained beta files for Yoshi's Island or sound files for Star Fox 64.
Combing through this stuff to find something specific like Star Fox 64 sound files is probably very cumbersome and the 'official' development archive of SF64 probably doesn't contain the same files.
Maybe it as the personal archive of an EAD employee, that they made a back-up of just in case.