I recently came up with a theroy: Luna and Nightmare Moon were originally two seperate entities, when NMM was defeated, the Elements of Harmony did not destroy NMM, but more rather, fused Luna and NMM into one being, this explains why Luna always referred to herself as "we" in the episode, referring to both Luna and NMM, this also explains why Luna sounded like two different people talking when she used the "Royal Canterlot voice", because it was both Luna and NMM speaking simultaneously.