I think making the Notmuch interface "pure" is a great design decision. By pure I mean that it just operates on tags, but never deletes or moves files and it doesn't even know about folders.
This gives it great flexibility. You can implement virtually any logic in a Maildir backend by remapping tags to actual files. Any arbitrarily complicated workflow, silencing, automated scoring like what Gnus offers, etc. is possible while the UI will be the same. Just tagging.
The problem is that Notmuch developers do not bundle any tools for implementing such a backend with notmuch, and third party stuff like afew [1] is lacking. It reminds me a bit about the situation with address completion. For a long time, mu offered this, while notmuch relied on hacky third party scripts.