I've never liked the way notmuch displays threads in #Emacs. Today I learned that "M-RET" displays the selected thread in a nice, threaded split view (notmuch-tree-from-search-thread).
I'd like to go back and learn this a couple of years ago, please.
@jbaty if you use the default notmuch-hello front end, you can configure a given saved search (virtual folder) to open in tree-view or unthreaded-view.