How can I comment comma-separated array values?

No, it’s definitely not okay to comment your code this way. It changes the string, and even though WordPress might strip the incorrect characters and yield the correct pages (it wouldn’t if your “comments” contained comma’s or numbers), it is incredibly unstable. Instead, if you do want to comment them, I would suggest storing them as an array, commenting that in the way you described, and implode-ing it with a comma:

$exclude_ids = array(
    41, // First page title
    43, // Second page title
);

wp_list_pages( array(
    'exclude' => implode( ',', $exclude_ids ),
) );