Glad you got it to work! Per my comment, WooCommerce takes Post Meta into consideration whenever deciding whether or not to add a Product to the Shop Catalog. It seems you were able to make it show up by updating the product visibility:
update_post_meta( $new_product_post_id, '_visibility', 'visible' );
I’m not 100% familiar with WooCommerce so should it take other post meta you can follow the references below:
Adding A Product To WooCommerce Programmatically
WooCommerce Update Product Visibility
There was a WordPress Stackexchange answer which listed a ton of Woo Meta but I can’t seem to find it :/