I am also having issues hiding hidden products from the search function. I have quadruple checked my install and have marked the category as hidden (several times). On top of that, I installed the optional file and limited the hidden category to hidden products.

The only file in this mod that intersects with the search function (as far as I can see, and I'm no coder) is tpl_advanced_search.php - and it only hides the hidden categories from the category dropdown selection on the advanced search page - if I search for my hidden category, the products still appear on the advanced search result page.

I'm assuming (and yes, I know how dangerous it is to assume) that changes need to be made to the advanced search result header to hide the products from the search results.

Is this the correct file to change to hide the products from the search function? I appreciate any feedback - even if it's in the form of a slap to the back of the head.