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If WooCommerce is not active, that is not an indication that WooCommerce customer data does not exist in the database. Perhaps the reason that it is deactivated is because everything else is too to try an get around the poor migration performance that you speak of. I wonder if a better check would be for the woocommerce_version option whether it exists or not e.g. https://github.com/woocommerce/woocommerce/blob/3.0.0/includes/class-wc-install.php#L225
The WooCommerce config file contains 50 keys (https://github.com/deliciousbrains/wp-migrate-db-anonymization/blob/5508a6c782b9efc8118562b5606b64bc3cec7d50/config/woocommerce.php). If WooCommerce is not active, each field is checked against these 50 keys in vain. With larger databases this will have a negative effect on the already poor migration performance.
My suggestion: Check whether WooCommerce is active at all before the config file is included.
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