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If I understood your question correctly¹, wrapping the action call inside a Class avoids the menu being displayed in all sites of the network.

¹
its only showing when i am in that blog => I understand that you mean: "it is not only showing..."
When i am in blogid:3 or blogid:4, i cant see that menu in blogid:2's list => I understand that you mean: "I can see the menu of blogid:2..."

/*
Plugin Name: The Menu Item
Plugin URI: http://wordpress.stackexchange.com/questions/55724/
Description: Add Menu Items to Admin Bar
Version: 1.0
Author: wordpress.stackexchange
*/

class Brsfl_55724_MenuItem
{

    public function __construct()
    {       
        add_action( 'admin_bar_menu', array($this, 'toolbar_link_to_mypage'), 999 );
    }

    function toolbar_link_to_mypage( $wp_admin_bar ) 
    {
        $menu_id = 'my_page';
        
        $args = array(
            'id'    => $menu_id,
            'title' => 'The Menu Item',
            'href'  => '#',
            'meta'  => array('class' => 'my-toolbar-page')
        );
        
        $args2 =  array(
            'parent' => $menu_id,
            'id'     => $menu_id . '-example',
            'title'  => __( 'Example Menu Item', 'example' ),
            'href'   => get_admin_url( $blog->userblog_id, 'edit.php?post_type=example' ),
            'meta'   => array('class' => 'my-toolbar-page')
        );
        
        $wp_admin_bar->add_node($args);
        $wp_admin_bar->add_node($args2);
    }
    
}
$brsfl_55724_MenuItem = new Brsfl_55724_MenuItem();