Solved it for anyone else who might find this useful…
//This is the query that gets the blocked Post IDs
$things = array();
$results = $wpdb->get_results( "SELECT sid FROM wp_entries WHERE uid = '$current_user->ID'");
foreach( $results as $result )
$things[] = $result->sid;
//This is the query that blocks the posts
$args = array('cat' => 8, 'showposts' => 3, 'post__not_in' => $things );
$category_posts = new WP_Query($args);
if($category_posts->have_posts()) :
while($category_posts->have_posts()) :
$category_posts->the_post();