Hide posts belongs to few categories in homepage

You can do this with pre_get_posts.
This hook is called after the query variable object is created, but before the actual query is run.

For excluding category id 32 and 39 from homepage, you can setup a function like this.

function wpse_exclude_categories( $query ) {

    if ( is_admin() )
        return;

    if ( $query->is_home() && $query->is_main_query() ) {
        $query->set( 'cat', '-32,-39' );
    }

}

add_action( 'pre_get_posts', 'wpse_exclude_categories', 1 );

EDIT

Although I would strongly recommend you to use WP_Query. But you can change your code to exclude category posts with query_posts.

$args = array(
    'cat' => '-32,-33',
    'paged' => $paged
);