I think one of the most confusing things about version 1.3 of the Options theme has been the missing navigation files. Of course, I've had a sticky post up about this on the Options theme forum to help users adjust.
There was one good reason for this major change — to allow for more change in the future. In the next version, I had planned to let users pick and choose which categories/pages they wanted to appear in their navigation menus from the Options Settings page.
The alternate route, which would require you to edit the files manually, is bringing back the old
sub-nav.php. This would entirely halt progress in this area, but maybe some things shouldn't be developed any further.
My proposal is to bring back the navigation files, so users can edit them manually. Rate up if you'd like to see this happen in the next version and would rather manually edit the files.