It is more likely to be fair use in this specific instance, as the copyrighted work to which the analysis is applied to is the whole game, not the code itself.

A big part of fair use analysis is in the effect on the market for the original work. If people have to obtain a copy to even use the project in any interactable way, the effect is either none (if we suppose every user of the project gets their original copy illegaly) or positive/benefitial to the copyright holder (if it makes those users actually buy legit copies)

The game is a copyrighted work, but so is the source code. The compiled code is a derivative work, and so is the decompiled code. Nintendo is not selling the source code, so arguing about sales in the market does not makes sense.

The fair use analysis is done on the work as a whole, the Zelda game that's registered on the Copyright Office. Not the code only.