For any game, the odds are that it has unused assets or partially completed systems that hit the cutting room floor.
https://arstechnica.com/gaming/2020/01/how-to-get-star-fox-6...
Ocarina of Time started with the Mario 64 engine, so there are probably bits and pieces all over.
I'm honestly curious, i've never actually heard any theories about Luigi and mario 64 other than he just cut due to above mentioned reasons. Much like Yoshi.
Why delete it? You never know if they might reinstate it (before release that is, and why bother deleting on release day?) or the model could be used in another game, making them costs money, storing them not that much.
The space obviously wasn't needed during development (this is leaked source, I don't know if it made it to the gold version) so there's two likely possibilities:
a) They knew about it but didn't have the dev/tester time to vet the change. This is coming from an era when most game testing was done manually and the N64 toolchain had some big issues around launch. Higher priority fixes might have just pushed a cleanup task like this off the list.
b) They just didn't know. This is also from an era where DCVS weren't particularly common in the games industry and CVS was still black magic in some circles so auditing changes or doing code reviews were very rare.
Also, as a developer (game and webdev), there's tons of leftover stuff. Most of which is assets. For games, the artists would've put them in the codebase at some point. For web, it's usually just forgotten when removing features.