Hi!
I’m assuming the Ecwid categories are custom taxonomy terms (like product categories in WooCommerce). While I’m not familiar with that e-commerce system, excluding a category (or in this case a term) should be not much different from any other taxonomy terms.
Basically, if you want to exclude certain posts/products/custom post types that belong to certain categories (taxonomies), then you can do it on the Advanced Options -> Exclude results panel: http://i.imgur.com/NjyaQs7.png
A bit more information could be also found in the Category and term based exclusions documentation chapter.
Let me know how it goes!