The way how Comment Reply Email Notification works is to add hooks to the WordPress comment handling – so whenever a comment is saved, the hook of the plugin gets called to check if the author of the comment subscribed to get notified about responses via e-mail.
If that does not work with WooCommerce than WooCommerce seems not to use normal WordPress comments but its own code to handle product questions – which makes sense since products are not blog posts or pages but a custom content type.
So far I don’t have any experience with customer questions and response in WooCommerce. The only WooCommerce setups I have ever done myself did not have this feature. So making my plugin compatible with it means I have to set up WooCommerce myself first and check how that works – and this may take a couple of hours. Time which I can not afford at the moment – sorry. But I’ll noted this as issue and maybe that will be implemented in future updates:
https://github.com/arnowelzel/worpdress-comment-reply-email-notification/issues/43
As always – pull requests for that extension are always welcome. The plugin is open source and anyone with PHP knowledge can participate!