Excluding Specific Terms from WP_Query
Your Tax Query is should be looking within another array.
'tax_query' => array( array( 'taxonomy' => 'categories', 'field' => 'slug', 'terms' => array( 'special-offers', 'other-terms' ), 'operator' => 'NOT IN', )),Rest of it seems okay.Check out the WP_Codex on this
Final solution was to add exclude and term id to the taxonomy arguments. Since it is for taxonomy and it uses foreach loop.
$args = array( 'parent' => 0, 'hide_empty' => true, 'exclude' => 13,);And answer for how to output custom post type posts with no taxonomy can be found here: http://www.codeforest.net/wordpress-tip-show-posts-no-category-term
Thanks to CBroe and ste for their time.