Are runs done on pc using the Cemu emulator allowed or not?

"All homebrew applications are banned, except for BotwRuns v1.0 found in the resources section." Read the rules.

however, cemu is an emulator, what if you could prove you are not using mods by showing the graphics packs sections and having nothing check marked.

Cemu does not emulate the Wii U with 100% accuracy.