I like to think that people in the pokemon world see legendaries as "endangered species," meaning there are still several left, but just a few. They are also probably creatures people surrounded their religions with, which could also be how they got their legendary status. But there are still some legendary pokemon that are indeed the only ones of their kind, mainly the more supernatural ones (like Dialga, Palkia, Giratina, etc.). Then there's pokemon like Mewtwo (made in a lab, once). Mythical pokemon are kind of the same way too (like how there are multiple shaymin, but only one Arceus).