Yes, you can use a master ball in a Nuzlocke challenge, but it is generally not recommended. This is because using a master ball takes away the challenge and fun of the Nuzlocke challenge. If you are struggling to catch a certain Pokémon, it is better to try and use other methods such as luring it with food, using a Pokémon with the ability False Swipe, or using a Poké Ball with a higher catch rate.