"Craft isn't installed yet" error after updating to Craft 3.1
Have you tried running ./craft setup to double check if your setup is correct? 

If ./craft setup completes successfully ./craft should find the existing installation and complete any required setup. 

In my experience, this is usually related to a non-default /config/db.php or problematic .env file.

Note: Always do a backup before trying anything related to setup just to be on the safe side.