modules: services: use new nginx wrapper

And when not possible, document why.

Note for the future: there is some repetition in some modules to
configure the correct value of the subdomain, which I happen to know
will line up correctly thanks to the nginx wrapper. A good way to
refactor this in the future would involve avoiding this repetition,
allowing use to query the correct domain in some way...

machines/porthos/services.nix

@@ -90,9 +90,6 @@ in
       enable = true;
       password = my.secrets.nextcloud.password;
     };
-    nginx = {
-      enable = true; # FIXME: remove this when done migrating
-    };
     # The whole *arr software suite
     pirate.enable = true;
     # Podcast automatic downloader