I may be wrong, but I doubt that anyone has implemented that number of repository modules within a single portal. I am not aware of any 'technical' reason it would not work. the only comment I have is that you might think about the overhead of maintaining that many unique instances of the module versus some small changes to the code which *might* allow you to have only 1 instance of the module and have the context of the module (categories, files, etc) filtered based on security roles...
not sure if that would work, especially if each instance will have separate unique categories, roles, etc. Certainly if the roles and categories where going to be duplicated across all those instances I would not want to have to perform the multiple maintenance required.
so, in summary, I see no reason why your structure would not work the way you've laid it out, however, I think it might benefit you to think about what changes could be made to the module to allow you to meet your goals through a single instance ( or at least a dramatically reduced number of instances ) of the module.