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You are correct -- the current version of Content Database does not support categories on folders.
Some good news: the next update (version 10.2.1) of Content Database does support this functionality via the API. (The default web GUI will not expose the new feature.)
For now, one workaround is to use a "hidden file" inside of each folder on which you wish to apply categories. Apply the categories on the hidden file, and then code your application to get the categories for that folder from the hidden file instead of from the folder itself.