It would be great to see Mudbox create individual materials for an imported object which match the materials of that object.  For example, if import a human head object, it usually contains a number of different material zones (e.g. Face, Scalp, Lips, ears, eyebrows, lashes, etc).  This would be useful because you could hide parts of the object by a material zone (e.g. the EyeBrows) in order to paint the forehead underneath the brows.

Actually I’ve requested this feature as well. It really is handy and helps manage large polycounts.  You can actually hide them individually but it’s not as easy as before. I’ve been creating selection sets to work around it.

Can you try and create Sets per face or per object in Maya before export of the obj.(In Maya Create>Sets>Set [option box] )

Make sure Groups and Point Groups are turned on in the Obj export options.

Mudbox will see the sets in the file and create selection sets for you. You can use these for hiding a showing parts of the model or various objects.