org-mu4e.el

(defconst ragone-unread-tag "unread"
  "Tag to add to Org elements which have unread emails.")

(defun ragone-tag-unread-elements ()
  "Update Org elements with `ragone-unread-tag' if there are unread emails."
  (unless (mu4e~proc-running-p)
    (mu4e~proc-start))
  (org-map-entries
   (lambda ()
     (let* ((search (concat "flag:unread " (nth 4 (org-heading-components))))
            (code (with-temp-buffer
                    (call-process "mu" nil (current-buffer) nil "find" search))))
       (org-toggle-tag ragone-unread-tag (if (= 0 code) 'on 'off))))
   t
   'agenda))

;; Add a hook to run before agenda displays.
(add-hook 'org-agenda-mode-hook #'ragone-tag-unread-elements)