Woocommerce – Override the default templates location under the theme directory

I believe you can use the woocommerce_template_path hook/filter:

// $path defaults to 'woocommerce/' (in your theme folder)
add_filter( 'woocommerce_template_path', function( $path ){
    $my_path = get_stylesheet_directory() . '/plugins/woocommerce/';
    return file_exists( $my_path ) ? 'plugins/woocommerce/' : $path;
} );

It should work whether you’re overriding only specific files or all — i.e. you copy all files and folders from wp-content/plugins/woocommerce/templates to your theme.