Generally, they don’t include intentional ones, or rather, haven’t done so since Super Metroid (and there, only with the wall jumps). When they release new versions of older games they often do so with patches to try to remove sequence breaks. And in new games they try to make sure not to include known older ways of sequence breaking, and sometimes include pretty drastic measures to prevent it.
Speedrunners sequence break anyway, because that’s how they are. But Nintendo gives every indication that they hate this for some weird reason.
Ah, here’s a YouTube link that goes into more detail about it: https://youtu.be/QLWKsugJPy4?si=gsT78aNb3wsQwCax
We’re still in the bad timeline where Biff went back in time with the sports almanac. That one doesn’t get flying cars.