1) Virtual libraries are built on search strings. If you create additional virtual libraries based on search strings which are strictly more restrictive than the original one, then you could think of them hierarchically, sure. But each is simply another Virtual Library, there is no hierarchy structure Calibre enforces upon them.
2) You are incorrect; you
can have hierarchical tags. Preferences → Look & feel → Tag browser → “Hierarchy and searching” tab → “Select categories with hierarchical items:” → Ensure “Tags” is checked (or whichever column you wish to use – below, I suggest that you may wish to use a custom column, instead). See also the
tutorial in the Calibre User Manual on managing hierarchical categories in the Tag Browser.
3) Again, see the
Calibre User Manual (hotlinked directly to section on search/replace while editing metadata for multiple books at a time). However, see also Preferences → Metadata download (in the Sharing group) →“Create rules to filter/transform tags”. Many rule types are possible including Remove, Replace, Keep, Split, and others. If you find yourself making the same replacements many times on your library's existing metadata, then adding rules here can help prevent the need for making those same changes again in future when downloading metadata for new books.
4) You may wish to create a custom column for the genre, rather than storing it with the rest of your tags. As mentioned above, you should have no trouble making this custom column hierarchical. Organizing genres into VLs should be very simple, though do make sure to read – you guessed it: –
the Calibre User Manual which will explain to you the particular syntax to use when searching values in a hierarchical field.