How can I add a custom class to only nav sub-menu > li > a items in WordPress?

To be applied to sub-menu items only, your code should be:

add_filter( 'nav_menu_link_attributes', 'nav_menu_link_class', 10, 2 );
function nav_menu_link_class( $atts, $item ) {
    if( !$item->has_children && $item->menu_item_parent > 0 ) {
        $class="has-ripple";
        $atts['class'] = $class;
    }

    return $atts;
}