There is no discernable difference between booting atmosphère through fusée and Hekate. The "Hekate is broken" meme comes from a dev's personal vendetta who disabled his software when it would detect a hekate-specific file. Just keep your shit...
Why is it so shocking that Nintendo uses DMCAs for the exact reason DMCAs exists? Sure it's unfortunate if you're a pirate but why would you expect Nintendo to not ask an employee to take 30 minutes to write a DMCA notice against a piracy tool?