Remove update messages for deactivated plugins

Yep Its possible if you hook a function to site_transient_update_plugins filter hook and check if plugin is activated using is_plugin_active like this:

add_filter('site_transient_update_plugins', 'remove_update_nag_for_deactivated');
function remove_update_nag_for_deactivated($value) {
    foreach($value->response as $key => $val){
        if (!is_plugin_active($val))
            unset($value->response[ $key]);
    }   
    return $value;
}