There is no SEF links related changes in Mobile Joomla 2.0, but there are changes in menu modules:
1. MJ's Mobile Menu module is considered to be legacy, i.e. MJ2 doesn't include this module, but updating from MJ1 to MJ2 doesn't uninstall it (for backward compatibility).
2. Instead, MJ uses Joomla's Menu module with customized layout file.
So, check that you use Joomla's Menu module (mod_menu), submenus are not disabled in its settings, and menu module is assigned to all menu items where it should be presented.