When you go to the PLugins > Blocks > Course Overview and disable the Removed From View filter, it does remove it from the dropdown list but does not remove it from the 3-dots menu.

See attached screenshot.

If the option to hide a course still exists, but this filter is disabled, then a student will never be able to see that course again because they can not unhide it.

Using Moodle 4.1.1+ with the Boost theme.