DB and operating system packages updates is it ok to apply security updates to the packages of the operating system that hosts an Oracle Database? Or is it better to not touch them, since the system is perfectly working? I have an Oracle Database installed on a Red Hat Enterprise Linux 6, on which some packages have security updates available, and I am not sure about what to do.
You should apply patches. Clone your database, apply the patches to the clone and see if it affects its operation. Test, test, test. But security patches aren't issued on a whim. Are they mandatory? Recommended or optional patches? But at some point you will have patches you do need to apply.