I know people who love to organize their icons on the desktop, and lay everything out there. It helps them find things back more easily. I think it's related to the method of loci where spacial categorization is a way to recall things more efficiently.
It would be interesting to try to tap into that. Maybe create different places with a way to navigate between them and place objects in them. It doesn't have to be exactly like reality, it would be too constraining otherwise. There could be shortcuts and different zoom levels to information.
Maybe there would be a static foreground like a desk that provides a work space and and reference anchor for the mind. And then the background could move independently, be a galaxy of information the user can sift trough using various tools.
One interesting development will be how symbolism will be developed. We need visual cues so we can recognize different kind of objects. This will help us navigate around and also know how to interact with each item. I don't think everything should be text, it's not be very practical in 3D.
But to answer your question, I don't think a file manager will exist (in the traditional sense). Right now each application takes over the whole environment but at some point there will be a second layer, a common environment that holds all the objects. This will be the normal OS-provided environment. The file manager will be replaced with tools that help you categorize and search the objects but it will be different because they would just interact with the universe like any other tool.
PS: Or maybe I'm thinking too much of Smalltalk