Using a default aegir installation for multisites I get the following errors:
foo$ drush omega-subtheme "foo" html5 --destination=foo.bar foo$ The destination is invalid.
Debugging includes/omega_tools.drush.inc shows me that the function omega_tools_sites() returns an array containing " => all" when sites.php is empty.
As a temporary fix, I added foo.bar to sites.php, but I still get the error. Using the fix in http://drupal.org/node/1338932#comment-5233574 lets me successfully create the subtheme in sites/foo.bar/themes/foo.
I still think omega_tools_sites() should let me use destination without these extra measures though.