Setting explicit permissions on Document Libraries in SharePoint?

I am creating SharePoint Team site, that is going to contain Document Libraries that are going to require explicit read/write and read/only permissions, based on the user accessing it. If I set explicit permissions for certain security groups on the Document Libraries, how that impact the permissions structure at the top level of the SharePoint Team site?

And is there a way for Document Libraries to be completely hidden from users that don't have any permissions to them?