There's a topic for questions~
Real Pokemon Guru, though the original guru doesn't come around much anymore, I'm still here, happy to try to answer. And yeah, this would fit in there.
But anyways.
For trans-dimensional beings, like Dialga, Palkia and Giratina, I'd say there's only one of each. Celebi has been observed to exist as a species, as per movie 4, and the Manaphy in Temple of the Sea would seem be a descendant of other Manaphy, as it started from an egg.