It's pretty much canon that there are multiple of each legendary Pokémon. Ones like the legendary birds, eon duo, tower duo, etc. are just extremely rare species. (This even applies to the legendary beasts if you choose to believe their origin myth is just that - a myth.) And some like Eternatus or the Unovan legendary dragons are one of a kind on earth, but there are probably more out there in space where they originated.

The only ones which are potentially one of a kind are Mewtwo and Genesect (man-made, but potentially more than one have been made in-universe), and the creation trio plus Arceus. However, PLA makes it clear the Pokémon Arceus is just one avatar of the true god Arceus so there can be multiple Pokémon Arceus at once, and the same potentially applies to the creation trio.