If there's only one of each fruit, how could Blackbeard recognize the "Dark Dark" fruit? If someone had seen it before you'd think it would have been eaten. 

And I also thought I remember a segment about no one knowing their fruit before they ate it. (I think it was with the CP9 arc)
I can't recall exactly when this was said during the series, but as the WIKI says here, when the user dies, the fruit he ate simply regenerates inside the closest appropriate fruit the same place where the user died and their ability is reborn into another fruit of the same kind instead of growing from a plant.

It's only my assumption but maybe CP9 did not know what the capabilities of their new fruit were because they were not so rare.

I think Blackbeard followed the progress of the user of Dark Fruit, so he knew when and where it is.