I believe that the Wavefront OBJ format specifies the maximum number of distinct materials as 512. However my experience has been that Poser's import can't handle that many. I'm not sure of the exact limit, but it's somewhere in the 300s. The way around that would be to split the mesh into separate sections so that each part has fewer material zones, and that would help a little with the material room navigation too.

As for your naming problem, my approach would be to hack the OBJ and MTL files as necessary. They may be inefficient, but in situations like these their  human-readable format makes search-and-replace relatively easy to do. You'll need a decent editor, of course: my recommendation is Notepad++.