I figured it out. Mojave introduced a new security measure, preventing any application reading certain user/system folders including photo, mail & message libraries.
Adding Duplicati.app to the list in System Preferences -> Security & Privacy -> Full Data Access seemed to have fixed it for me. I’d like to hear if others were having the same issue.
Also I think for a future Duplicati release there should be a warning, giving users a heads up they need to give additional permissions to the application if they are on Mojave.