Tested on woocommerce 3.0.4

function my_woocommerce_taxonomy_args_product_tag( $array ) {    $array['hierarchical'] = true;    return $array;};add_filter( 'woocommerce_taxonomy_args_product_tag', 'my_woocommerce_taxonomy_args_product_tag', 10, 1 );

Found the solution, here it is if someone is looking to do the same:

function reregister_taxonomy_pro_tags() {    # the post types that the taxonomy is registered to    $post_types = array('product');    # set this to the taxonomy name    $tax_name = 'product_tag';    # load the already created taxonomy as array so we can    # pass it back in as $args to register_taxonomy    $tax = (array)get_taxonomy($tax_name);    if ($tax) {        # adjust the hierarchical necessities        $tax['hierarchical'] = true;        $tax['rewrite']['hierarchical'] = true;        # adjust the hierarchical niceties (these could be ignored)        $tax['labels']['parent_item'] = sprintf(__("Parent %s"),        $tax->labels->singular_name);        $tax['labels']['parent_item_colon'] = sprintf(__("Parent %s:"),        $tax->labels->singular_name);        # cast caps to array as expected by register_taxonomy        $tax['capabilities'] = (array)$tax['cap'];        # cast labels to array        $tax['labels'] = (array)$tax['labels'];        # register the taxonomy with our new settings        register_taxonomy($tax_name, array('product'), $tax);    }}

init action with a late priority so other taxonomies are loaded

add_action('init', 'reregister_taxonomy_pro_tags', 9999);

Thanks for the above answer saved me a ton of research but you should replace

    $tax['labels']['parent_item'] = sprintf(__("Parent %s"),    $tax->labels->singular_name);    $tax['labels']['parent_item_colon'] = sprintf(__("Parent %s:"),    $tax->labels->singular_name);

to

$tax['labels']->parent_item = sprintf(__("Parent %s"),$tax['labels']->singular_name);$tax['labels']->parent_item_colon = sprintf(__("Parent %s:"),$tax['labels']->singular_name);