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Nintendo is still selling Mario 64 in various ways. You can buy it in "Super Mario 3D All Stars" for $60 on the Switch.

Nintendo, like many other Japanese companies, are very protective of their IP.

That assumes they even still have it. Not sure about Nintendo in particular, but many other games of the era are known to have lost source code.

Nintendo did (supposedly) use an emulator for the N64 games in Nintendo Online (for the Switch); so it's possible that they don't have the source (or maybe it had enough machine-specific code that doing a source port would be more effort).

Of course, if they can re-sell it as a subscription service they probably would want to avoid releasing the source anyway…

Virtual Console (or whatever Nintendo calls it now) releases mean that the game can be a moneymaker decades past the end of retail sales. You also see this with MS-DOS games, sometimes modders will voluntarily stop making their fan patches if an official rerelease makes it to Steam.