I recently created a Modern Team Site and we want to have a second Pages Library with different permissions to the default page library, is this possible, there are no options to add an App and create a page library and if I switch back to classic, I can only create A WIKI page library and can't add the Site Page content type to it. My first thought was to create a folder in the default page library but that option isn't there either.
The Site Pages library by default is public because that's where your News articles (as well as your site pages) are managed. Audience targeting is coming soon for modern web parts (here's the uservoice entry on that). So for the time being, and keeping with managing permissions on containers vs individual pages, creating a folder is the next best option. This is turned off by default in new modern page libraries, but you can turn it on by going to your Site Pages library / Gear / Library Settings / Advanced Settings, and toggle Make New Folder available to Yes. Good luck!