To hide the shortcuts for each module you have to open menu.php file individually for each module which you can find under /modules/menu.php. And then just comment the line which you want to hide it, for example right now I am hiding Create Account so I have commented the following line under menu.php

global $mod_strings, $app_strings;

// if(ACLController::checkAccess(’Accounts’, ‘edit’, true))$module_menu[]=Array(”index.php?module=Accounts&action=EditView&return_module=Accounts&return_action=DetailView”, $mod_strings['LNK_NEW_ACCOUNT'],”CreateAccounts”, ‘Accounts’);

if(ACLController::checkAccess(’Accounts’, ‘list’, true))$module_menu[]=Array(”index.php?module=Accounts&action=index&return_module=Accounts&return_action=DetailView”, $mod_strings['LNK_ACCOUNT_LIST'],”Accounts”, ‘Accounts’);

if(ACLController::checkAccess(’Accounts’, ‘import’, true))$module_menu[]=Array(”index.php?module=Accounts&action=Import&step=1&return_module=Accounts&return_action=index”, $app_strings['LBL_IMPORT'],”Import”, ‘Accounts’);

?>