Why is that even happening aside, from quick look at core it does the following to achieve that in WP_Posts_List_Table class:
$sticky_posts = implode( ', ', array_map( 'absint', (array) $sticky_posts ) );
$this->sticky_posts_count = $wpdb->get_var( $wpdb->prepare( "SELECT COUNT( 1 ) FROM $wpdb->posts WHERE post_type = %s AND post_status NOT IN ('trash', 'auto-draft') AND ID IN ($sticky_posts)", $post_type ) );
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