Those are all KNOWN, physical and separate Library Structures on your disk.
I say Known, because there is no limit on how many Libraries you can have (
would be a nightmare to maintain), only how many Calibre can interact with Quickly (those on the list).
FWIW Delete Library only removes the entry from the list, not the structure.
BTW that list also is consulted other places (plugins). eg CopyToLibrary only allows the Target to be Known Libraries (you can open any Library from the command line,without it being on the list)
Tags:
They are there to help you, NOT to sell books (by stupid keyword search with every synonym or typo) or replicate old style Card Catalogs
Normalize your data. You do not need 42 ways to spell Magic. 19 permutations of Werewolf...
I also decide whether to us a Singular or Plural version for a tag (I lean to Singular)
and IMHO the most dumb one of all '
Fiction. Science Fiction'
My Library is mainly
Fiction. I do not need to tell anyone that Fantasy (the tag) is a subset of Fiction. Gone
Non-Fiction (preface is used to separate those from the Fiction use of the keyword) Non-Fiction.Biography.Fantasy Writers
and FYI Calibre is a Relational Database. What you see is a Flatten Display of the data
When you make a column entry. it adds or reuses the base table Definition (Use of the
Manage context in the
Tag Browser allows for renaming, whilst not breaking the Usage) for that column. And if you
rename to an existing Tag, it merges the usage, thus making that activity, simple. (I routinely go thru mine to weed out those that slip thru my Intake process)
Fantasy gets an
Index#, any book that gets Tagged Fantasy, really links to the Index (long Int, not the text). Very data file efficient
Consider reworking to a tighter set of Libraries that address
1)Security (little eyes, Classified ...)
2)Structural (additional columns, or different fixed data allowed) needs not covered in basic metadata AND only used by a tiny subset of entries. Technical Publications need specific items tracked.
Columns are for fast searching and ordering. There are tools to search Comments (slow) for obscure terms