An introduction to what is what:
No, those are libraries that the projects xyz.pro file has listed as available component libraries (*).
The components (symbols) that are being used by the schematic are stored in the projects xyz-cache.lib file.
*) EEschema currently doesn’t know a global component-library-table file that is being used for global symbol libraries.
This information is stored in a file called template.pro (with absolute paths) and when you create a new project will be the template for the projects .pro file.
If you change the template.pro file after the creation of the project those changes are not adapted!
To solve your trouble there you can either find those libs and put them into the folder where they are searched for in or open the Component Libraries dialog (EEschema) and get rid of those entries.
For checking an existing project they are not needed.
As for the footprints, @dchisholm should be on the money.
PS: we really should be starting to call components symbols.. it’s getting messy.
Components are parts with linked footprints IMHO.
Might need to ask @c4757p or @SchrodingersGat about that one.. 