Another couple of noob questions, why has it taken 23 years? What's the actual importance of this?
To add to what caff said - to put it in more layman terms, the game you get on a disc/download is like a very "mixed down" version of the game's actual files/content.
Imagine when you hear a music track on the radio - you just hear a WAV or an MP3 right? It's just a sound file. A flat waverform. Some 1s and 0s.
But on the producer's computer are all the "stems" - each individual sound file for each instrument/layer of the song at very, very high resolution. These are all "flattened" into one sound for the final output. In addition, more importantly, there will be an intelligent "project" file for whatever production software they use, which grabs all those "stems" and puts them in at the right places, with the right programming logic, with the right effects and compressors, etc, etc - and they can hit the Export button to "compile" all the sounds and logic into one flat audio file.
A game file is pretty much the same. On a disc/download, you've got the very purest "output" of the game's content. Just the engine logic required to run, just the assets required to show, just the script/logic files required to make it happen - all mixed down into a few assets and a flat "executable" for the game's running.
But on the developer's computer? A mass of other files - the full game engine, many versions and iterations of assets, ten times more script files used to pull everything together.
So the fact they've managed to retro-engineer a "decompile" of SM64 basically means they, for the first time ever, have managed to get SOME version of what was on the developer's computer at the time of final compile. They can pull apart all the parts and scripts and really look at them straight-on, without any obfuscation. Basically they've opened the black box that is the game's software. This will let them dig into stuff better - and more importantly (yet more dangerously) they can recompile/reconfigure the game basically however they want. This will include making .exe files which will run immediately on any machine with any hardware, the ability to tweak/adjust any systems and assets, etc, etc.
For Nintendo - pretty terrifying.