I minimise when I want to get the content, fx a VS code workspace, out of the way to retrieve it later.

Close is when I am done with that particular window/workspace.

Command+Q is when I’m done working in VS code entirely.

> what is the difference then between closing and minimizing?

Closing is putting away, as in “I don’t think I’ll need it in the near future”, and minimising is putting aside as in “I’ll probably come back to this in 5 minutes”. The minimised window is not cluttering the screen but still accessible from the dock and list of open windows in its application. This is not related to the problem you claimed to have with an application being still open without having a single window.