Try using a different way to set
org-agenda-files. The form you show above calculates the list at initialization, so any newly created journal files are not part of the list: you would have to add them manually.
In general, Org mode calls the function
org-agenda-files when it needs to calculate the list of agenda files. In the case above, if you evaluate
(org-agenda-files) i.e. call the function, you will get the list that was calculated at initialization. But if you look at the doc string of the variable
C-h v org-agenda-files, you will see that:
If an entry is a directory, all files in that directory that are matched
by ‘org-agenda-file-regexp’ will be part of the file list.
So you can set it in your init file like this:
;; either ...
(setq org-directory "~/org/")
(setq org-agenda-files (list org-directory))
;; ... or more directly without the variable
(setq org-agenda-file '("~/org/"))
In conjunction with the default value of
org-agenda-file-regexp which matches files that have an
.org suffix, this will ensure that the list of files that
org-agenda uses will include all files under the indicated directory with a
.org suffix, including any newly created ones (something which your current form does not do).
You might end up with a very slow agenda if you have all (or lots of) your Org mode files under that directory, particularly after a couple of years of journaling. But that's a problem for another question.