^ Technically speaking you can't use a shiny. The Shiny Clause stats that you can at anytime in the area you found it, catch the shiny but CANNOT use. However you can jailbreak this rule as that part isn't official. Marriland did it for his Nuzlocke. >>;
that's actually entirely subjective to who's doing the nuzlocke itself, and typically if I find a shiny I'd use it (i've only ever gotten two legit shinies anyways, one in my gold nuzlocke and one in heartgold. johto is magic)