Thanks for your nice words about the CJT plugin. I am pleased to hear you are using it on many of your websites.
This is a great suggestion, and you are right that it is a good idea for CJT to play nicely with highly popular plugins such as WooCommerce. In fact, we have had a similar request posed before with this plugin here: http://codecanyon.net/item/youtube-wordpress-plugin-video-import/4429742 where the user could not get the category custom type to appear.
I believe in order to get this to show, we would need to further enhance the custom posts feature of CJT to support additional taxonomies for other plugins.
I will try to schedule this development in the near future. Thanks again.