Namine isn't some god-entity with powers over everyone's Memories. Her powers are, when looking at it from a universal point of view, quite limited.
She has powers over Sora's Memories, and the Memories of those who are related to Sora.
None of the Nobodies in Castle Oblivion ever met Sora, so Namine couldn't affect them.
Think of Memories people share as train tracks, and the people themselves as stations. Anyone Sora met and bonded with is a 'station' Namine can reach by following the tracks - in our chase, the chains of Memories that connect the two.
Even when the Org members met Sora, it was still not enough for Namine to use it against them.
And then, of course, comes the interesting issue of whether or not she even could, seeing how the only Nobody whose Memories she messed with was Roxas - both Sora's Nobody, as well as a Nobody with a Heart...