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This is still pretty much headcanon territory.
Even if you consider the anime/game/various manga as separate canons they don't have clear answers.
My personal theory is that legendary pokémon are physical manifestation of things, from ideals to natural elements.
They aren't born, they "spawn", so while naturally they should be unique more can exist at the same time.
Then there are pokémon that are called legendary but really aren't, like Genesect.
Once there were many of them but because there is only one alive in the age of the games it's considered legendary.
