They previously "allowed" it at Evo 2013 after massive backlash from trying to shut down the Melee stream, years before anything related to sexual misconduct was talked about. There is nothing recent enough about how they treat the Melee scene to blame emulators or sexual misconduct, it's been documented to be happening since the scene was revived post-brawl.
The evo shutdown was presumably attempted to avoid any comparisons between their newest game (Brawl) and Melee; similarly, the recent shutdown probably has more to do with how bad Ultimate's online is compared to emulated Melee, rather than the mere fact that they're on an emulator in the first place. Other emulated online Melee tournaments without Ultimate have gotten away with it so far.
The evo shutdown was presumably attempted to avoid any comparisons between their newest game (Brawl) and Melee; similarly, the recent shutdown probably has more to do with how bad Ultimate's online is compared to emulated Melee, rather than the mere fact that they're on an emulator in the first place. Other emulated online Melee tournaments without Ultimate have gotten away with it so far.