Set the products_weight on that category of products to 0 ...
Then, you can test in your shipping module for if there are 1 or more Products that use the master_categories_id that matches your Category for the Flat Rate categories_id in the order and if so, add on to the calculated shipping cost ...
In the shopping_cart class is a function that should be able to help you:
Code:
/**
* Method to calculate the number of items in a cart based on an abitrary property
*
* $check_what is the fieldname example: 'products_is_free'
* $check_value is the value being tested for - default is 1
* Syntax: $_SESSION['cart']->in_cart_check('product_is_free','1');
*
* @param string product field to check
* @param mixed value to check for
* @return integer number of items matching restraint
*/
function in_cart_check($check_what, $check_value='1') {
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