The reason you have all the notes together in a zettelkasten is that you do not know when a piece of information will be relevant in the future. You may find the desire to elaborate on it or connect to it 5 years from now. For example, see my post on an timeline for learning about storytelling using the zettelkasten.
I don’t think there is a problem with having the two systems as long as you have an easy way to update links as you move notes between folders. It is also important to not archive your notes such that you no longer have easy access to them. If you archive them in such a way that you don’t automatically search them then that is a problem. But Obsidian searches all folders in a vault, so I don’t think that should be a problem.