Actually - it's not a question so much of removing them.... it's the issue of the "shown in navigation pane" option is not actually "clickable" when it should be.... I do use the Libraries feature (for custom ones) - but I don't want to see the Default libraries (music, videos, pictures) there since they're totally irrelevant to the usage of the DAWs. (digital audio workstations)..
If you look at the OP's pictures above - he's showing the properties pane for a library folder - the "shown in navigation pane" checkbox is supposed to be enabled so that it can be set on or off, but instead it is greyed out and permanently set to ON.
I'm in exactly the same situation as he is - on one of my machines I can set the "shown in navigation pane" option on or off at will, but on my second machine, the option is greyed out and set.
I am logged-in on both machines as Admin, so it can't be a rights issues, but something is different between the two.
I use Registry Mechanic and cCleaner regularly to keep the registries clean on both machines without problems and I've looked through all the user rights policy settings to see if there's a config to control it, but couldn't find anything....