Delete variations" action does not actually deletes variations

For some reasons the $variation->delete(); statement has disappeared :).

So, to delete orphaned variations on an existing product just check in any variation on the product/N/variations page and apply Delete variations actions action. If there were some orphaned variations then the warning will appear. Just press the CANCEL AND BACK button and you are done with the cleanup work.

The things a little more complicated if you've already deleted a product with orphaned variations. If you are totally sure that ALL (!sic) your variations must have a parent product then execute the code below:

foreach (\Drupal::entityTypeManager()->getStorage('commerce_product_variation')->loadMultiple() as $variation) {
  if (!$variation->getProduct()) {
    $variation->delete();
  }
}