I can't reproduce this. I've uninstalled Hathor and still have the sidebar.
The sidebar code uses the new JLayout feature. The overrides folder is at \administrator\templates\isis\html\layouts for the Isis template, but if there is no override, then the layout is searched for in the root \layouts folder.
If you aren't getting the sidebar after uninstalling Hathor, ensure you have a file at \layouts\joomla\sidebars\submenu.php. If you do not, then you possibly have a corrupt installation.