

Yep, even going way back, there are differences between speedrun times for Ocarina of Time on N64, Ocarina of Time on GameCube, Ocarina of Time on Wii VC, and Ocarina of Time on NSO. And that’s also not considering the native PC port recently assembled by the community.
And that’s why speedrun leaderboards always factor in game version/region and platform when measuring runs against one another.
Those sorts of things can absolutely happen. Newer versions of games often either patch issues on older versions or there may be some glitches that are not as easy to take advantage of when the hardware isn’t struggling as much.
The Zelda Speedruns site even maintains a list of version differences for various Zelda games which make a difference to which version is optimal to run.