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Probably most source code has been lost. Games were considered throwaway projects, executives barely knew what source code was, and game dev work was considered entry-level and low-status. The main source of 80s and early 90s code that we have are floppy disks that developers took home rather than the companies that published the games.

Consider that version control was something that was basically only used by Unix developers back then. E.g. DOOM, with a particularly technically proficient team, was developed by passing disks with source files around.

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Sonic Advance 2 might be late enough that developers started to take that seriously, e.g. I recall hearing that earlier games like Ocarina of Time already were being developed using CVS, for instance, and another game from around that time that I specifically recall would be Pokemon Diamond & Pearl, developed in an SVN repository

This may be true, but since the game was published by THQ in the west who then went bankrupt, no one knows who owns the rights to this game and so no one is likely to ever release it. If source was ever released we still wouldn't use it in the decompilation since that then becomes much more of a legal issue.

The spongebob movie GBA source was released recently: https://archive.org/details/the-spongebob-squarepants-movie-...

I was a gamedev in the mid-90s. We were using Visual SourceSafe, which was my first exposure to source control, but clearly others at the studio had been using source control for some time, so it must have been around in game dev for a little while before that, at least.