How to theme maintenance page for omega subtheme?
There's always a parent template, even if you don't see it in your base_theme.

The inheritance will go:


omega_subtheme template of NAME 
then omega template of NAME
then drupal core template of name


So you'll need to copy the drupal core templates. They can be found in

DRUPALROOT/modules/system


You can find page.tpl, maintenance-page.tpl.php and all the base templates.