Rayquaza- There was a shiny Rayquaza in the Hoopa movie, yet there was a normal rayquaza in the deoxys movie.
Also...Diancie- although mythical and not legendary, it's still rare. Yet, Diancie is formed by a mutation in Carbink, meaning there can essentially be more than one Princess Diancie.
Solgaleo/Lunala- Are legendary on our world, yet there are wild cosmog in the alternate dimension where they come from.
Legendary Dog Trio- Shiny versions of them can be seen in the zoroark movie, yet in pokemon chronicles Gold/Ethan encounters a normal Raikou(If I can remember correctly), and Ash has seen a normal colored Suicune and Entei in their respective movies.
Zekrom/Reshiram- This is my personal theory....in the Hoopa movie Zekrom and Reshiram can be seen well and alive, yet Kyurem could still become Black/White Kyurem even though it needs to absorb the two in stone form......soooo maybe there are multiple Zekrom and Reshiram?
My answer is: yes. I do believe there are multiple legendary Pokemon. However, to an extent. If anything, maybe all the legendary Pokemon have more than one each, even Kyogre and Groudon. However I think it stops with the creation trio as well as with Arceus, they may be the only ones of their kind. But as for the rest, definitely more than one each. Just my theory though.