I agree that duplication is not necessarily bad, it just makes it a lot harder to browse the module section on drupal.org to find relevant content, and this is what is really wasting a lot of time for users and developers.

It is my impression that the current "module categories" taxonomy is not really helpful because it has become too coarse to categorize the 2000+ modules that are out there, and a quick informal survey of my co-workers showed that others feel the same about this. Many of these module categories have a couple hundred modules, and their listing spans more pages than the average user is willing to read in order to find what they want.

Would it be possible to simply turn this taxonomy into a free-tagging field, or add a separate free-tagging taxonomy? We would then have terms that can categorize modules much more specifically, but more importantly we would have a way to link similar modules together.