After all, it was due to a MySQL timeout. I installed MySQL on the same Linux box to resolve this. I still don't understand why this happened suddenly after the update. My best bet is on Restarting my VM(droplet) @ digital ocean triggered something.
Enabling PHP FPM slow log helped me to understand the slow response due to the MySQL connection issue.
The most time taken process in your listed commands are:
Upgrade: php bin/magento setup:upgrade
Di Compile: php bin/magento setup:di:compile
By doing 2 basic tasks you will speedup your these commands.
First: Change mode to production (if it is default or development)
php bin/magento deploy:mode:set production --skip-compilation
Note: If your project is ...