As per my knowledge hot fixes are released to fix the defect pertaining to product(tridion). Presently we are using many CME extensions and workflows in our tridion implementation. Is there any way, except manually testing, to make sure if all the custom code/workflows etc are intact and working fine after any tridion hot fix?
This is no different from testing your own code - develop a test plan and execute it whenever you change anything. Ideally, automate your testing (using tools like Selenium, for instance) or custom-written test cases which you probably should write for back-end stuff like workflow automation.
Hotfixes are intended to fix a given behavior and are not always fully regression-tested (as typically there is someone on the other end of the phone line waiting for an urgent fix), and these hotfixes are then packaged on Hotfix-Rollups which are regression tested.