If you want to only display menu items at a certain level, we don't have a current way to do this. However, the following code change could get you started with showing just the items on the first level of the menu. You can tweak it to show however many levels you want. If this works for you then I can add an issue to our tracker to add a setting as an enhancement to a future release.
In /modules/mod_sclogin/helper.php:
1. Around line 559, replace
foreach ($menu_items as $menuItem)
$menuNav .= $this->getUserMenuItem($menuItem);
with
foreach ($menu_items as $menuItem)
{
if($menuItem->level=="1")
$menuNav .= $this->getUserMenuItem($menuItem);
}
2. Make the same change in the for loop that was around line 576.
There's not really a concept of a "hidden" menu item. When we attempt to fetch the menu items from the user menu that's selected, Joomla determines the appropriate items to display based on the user's group and the menu items' permissions. Besides limiting to just displaying a certain sublevel of the menu items, there's not much we can do besides advising you to split the menu and submenu up or to create a special menu to use for SCLogin.
-Melissa