At first I was gonna go "Mangekyou's are supposed to only be had by a couple people."
But then I remember, Kakashi's eye isn't his own, and he was still able to turn it into a Mangekyou. So theoretically, Danzou could have turned all those Sharingan's into Mangekyous.
I suspect that the eyes came from all the Uchiha that Itachi murdered. He didn't take the bodies with him, so I could totally see Danzou having ROOT collect their eyes and saving them for later.
I assumed he brought them into black pillar world, but they weren't there when he went to get Sasuke. Then again, it's another dimension or something, who knows how big that place is.