Developing plugin, where to place action hooks etc?

You do it like in your first example

// Shortcodes.php file       
function myplugin_shortcode( $atts ) {    
    if ( !empty ($atts) ) {
        foreach ( $atts as $key => &$val ) {
            $val = html_entity_decode($val);
        }
    }
    myplugin_display_items( $atts );       
}

// Register shortcodes
add_shortcode( 'output-items', 'myplugin_shortcode');