Majora's Mask should have a legit CIA.
You didn't get all the MM N3DS hype for nothing.
MM3D only has an EU legit CIA. There was no US one. So, in order to play MM3D via legit CIA on your US console, you gotta do some finaggling with your emuNAND to change it's region.
My current setup is 4.x PastaCFW, rxTools US -> EU 9.7 emuNAND and a 9.2 NAND dump I swap to when I feel like tinkering with a non-CN alternative for Pasta.