would the 60fps hack from cemu be allowed during master sword, dungeons and towers extended bug limit

CEMU and all other emulators are not allowed for speedrunning Breath of the Wild.

In adding to that, the some of the physics in the game is linked to the frame rate and would give you many disadvantages, along with a few advantages.

Yeah even standard Emu restrictions aside the 60fps hack changes the actual gameplay and handling due to how it's physics work, it's not just a quality of life thing so I doubt we'll ever see it even on an unofficial side leaderboard.