There are posts on this here and here, but my search does not turn up an idea-station suggestion, so please either point me to one if it exists or consider this a suggestion!
It would be nice to be able to change the visibility of sub assemblies within linked files. You can turn on/off an entire linked file's visibility, but you can't turn off individual subassemblies (if they exist) within a linked file, from the linking master file.