I'm assuming you are referencing Finder windows and not App windows. I see the same behavior with my Mojave system. High Sierra and earlier did not reopen the Finder window.
The Chrome default installation is to automatically start up when MacOS starts up. I think I disabled the app from starting up under System Preferences > Users & Groups > (select the user account) > Login Items.I'm talking about apps like Spotify, Messages, Chrome, etc.