I don't know if that is possible.
The boxes never bothered me though. Level design is a pretty abstract process anyway, and I believe that is why they originally chose boxes instead of models.
Edit; Netradiant does show the models for Doom 3, though, so it might just be a setting somewhere. I don't know if this can be changed in the config files though, or if it is hardcoded in the editor itself.
Edit 2: I asked Lord Havoc, and he told me that the models are set in the entities.ent file (in the gamepack). This makes sense; so if you guys want to see the models in the editor,
someone will have to create a custom entities.ent file that includes the model paths. Look at the Quake 3 entities.ent file for an example how this should be done.
Edit 3: This makes it possible to very accurately place items on desks, shelves etc, just like it's done in Doom 3. Of course Quake's ammo boxes are comically large, so they would look weird on a table and would never fit into a shelf, and Quake's weapons float in mid air so can't be placed onto a surface in a believable fashion. Someone should volunteer to change this, too. :-s