Remove all empty categories in WooCommerce

run.sql

-- Run this SQL commands from PhpMyAdmin or similar ways
-- change the wp_ to your tables prefix to make it works
-- Script from SalesGen.io 

DELETE FROM wp_term_taxonomy WHERE taxonomy = 'product_cat' AND count = 0;
DELETE t FROM wp_terms t LEFT JOIN wp_term_taxonomy tt ON tt.term_id = t.term_id WHERE tt.term_id IS NULL;