Deoxys is not required to completed the Hoenn PokeDex, however it is required to complete the National PokeDex.
>Have owned all (Generation VI) Hoenn Pokédex Pokémon except Rayquaza, Jirachi, and Deoxys.
>Have owned all Pokémon except Mew, Celebi, Jirachi, Manaphy, Darkrai, Shaymin, Arceus, Victini, Keldeo, Meloetta, Genesect, and Diancie.
So to answer your question, no! Deoxys no longer counts as an event Legendary (at least in ORAS), as Deoxys was not required to complete the National PokeDex in X&Y, but is required to complete the National PokeDex in ORAS.