Hi Venus. Although we have added a few more folder, at least at this point we are handling is about the same. I don't see us changing our structure anytime soon, since you get to a point where too many things rely on the path, but I'll be curious to see if you get any other input from users.
Unlike some of the sample above, the agency owned data isn't as complicated enough to need a category structure, at this point. We do have basemap services, etc., but typically those are for in-house use for the convenience of our users, and for web maps/apps. I just keep those with the _public name and access them thru our non-secure web adaptor. Easier for me to keep track, but Ihave to admit, I think about it from the internal organization of things and not from the public user since in most cases they will be going thru some other gui. But, again, "we" may rethink that as we get more services/data online.
I know I am struggling right now on getting OpenData to use/access our secure services since there is no way for it to reference our local proxy file. So trying to change things behind the scenes, and that may change (add to) our structure.