You can show only actual menu items for users.

[snenko]

if you add isShowTopLevelMenuItem function into Vtiger_Menu_Model class:

`
public static function isShowTopLevelMenuItem($menu)
{
if(isset($menu['childs']) && count($menu['childs'])>0) {
foreach ($menu['childs'] as $id=>$subMenu) {

	$privilegesModel = Users_Privileges_Model::getCurrentUserPrivilegesModel();
	if(\App\Module::isModuleActive($subMenu['mod'])==false) {
		continue;
	}

	if ($privilegesModel->isAdminUser() ||
		$privilegesModel->hasGlobalReadPermission() ||
		$privilegesModel->hasModulePermission($subMenu['tabid']) ) {
		return true;
	}

}
return false;

}
return true;
}
`

And update TPL file:
/layouts/basic/modules/Vtiger/menu/Label.tpl

` {if $MENU_MODULE=='Settings::Vtiger'}
{assign var=SHOWITEMMENU value='true'}
{else}
{assign var=SHOWITEMMENU value=Vtiger_Menu_Model::isShowTopLevelMenuItem($MENU, $MENU_MODULE)}
{/if}

{if $SHOWITEMMENU=='true'}

<li class="tpl-menu-Label c-menu__item js-menu__item nav-item menuLabel {if !$HASCHILDS}hasParentMenu{/if}" data-id="{$MENU['id']}" data-js="mouseenter mouseleave">
	<a class="nav-link {if $ACTIVE=='true'}active{else}collapsed{/if}{if $ICON} hasIcon{/if}{if $HASCHILDS == 'true'} js-submenu-toggler is-submenu-toggler{/if}" href="#"
			{if $HASCHILDS == 'true'} data-toggle="collapse" data-target="#submenu-{$MENU['id']}" role="button" aria-haspopup="true" aria-expanded="{$ACTIVE}" aria-controls="submenu-{$MENU['id']}"{else} role="heading"{/if} >
		{$ICON}
		<span class="c-menu__item__text js-menu__item__text" title="{Vtiger_Menu_Model::vtranslateMenu($MENU['name'],$MENU_MODULE)}" data-js="class: u-white-space-n">{Vtiger_Menu_Model::vtranslateMenu($MENU['name'],$MENU_MODULE)}</span>
		{if $HASCHILDS == 'true'}
			<span class="toggler" aria-hidden="true"><span class="fas fa-plus-circle"></span><span class="fas fa-minus-circle"></span></span>
		{/if}
	</a>
	{include file=\App\Layout::getTemplatePath('menu/SubMenu.tpl', $MODULE)}
</li>

{/if}`

[snenko]

I try to implement this via custom override code in my project.
But I think "custom" override functionality is not working for layouts and models.
So, each Yetiforce's updates remove my changes from the core folder

[vovpff]

Hm. For 5.3 if module inactive for user profile then this module invisible in menu