@styr,
Well technically the product categories are just like any other taxonomy within WordPress. So for starts in wp-admin under Simply-Exclude > Settings you should see the panels for Product Categories (product_cat) and Product Tags (product_tag) which are the taxonomies registered by WooCommerce. On both panels ensure you have the option “Show the extra columns on the Taxonomy listing and the Taxonomy edit form?” set to ‘Show’
When you navigate to Product Categories terms listing (Products > Categories) you should see the column added by Simply-Exclude.
Now as far as actually excluding taxonomy terms this is going to be dependent on who WooCommerce functions. I’ve not tested this and understand the Simple-Exclude plugin was written to work with the standard WP_Query object. If WooCommerce ignores the default WP_Query used internal to WordPress and does what some themes like Thesis does then there is not help I can provide.