In this line you are getting only the count of published items (obviously!!!!):
$published_projects = $count_projects->publish;
You should do something like this:
$count_projects = wp_count_posts( 'apps' );
$published_projects = $count_projects->publish;
$draft_projects = $count_projects->draft;
$total = $published_projects + $draft_projects;
More details and examples in wp_count_posts()
reference.