However, to be able to hide some Libraries is not straightforward, as it is not supported by the app itself, and there's a plugin that allows you to do so for 1 Library for free and pay for the others (It called Lock for Plex).
I used this extension and find out how it works, and I hacked it and be able to hide more than one Library.
How "Lock for Plex" work is by updating the database used by Plex.
It uses two bash files, one for lock and the other for unlock:
Plex Media Server/Plug-ins/Lock_for_Plex.bundle/Contents/Resources/lock_support/lock.sh
Plex Media Server/Plug-ins/Lock_for_Plex.bundle/Contents/Resources/lock_support/unlock.sh
Here's the content for myself after I've been modified on this file:
One other way to achieve the same result is to have some other disk partition and mount it on-demond.