Adding node_type condition as following:
db_update("node")
->fields(array(
'comment' => 2,
))
->condition("type", "node_type", "=")
->execute();
I can run the above with drush scr filename.php
Alternatively I could update with SQL query:
UPDATE node as n LEFT JOIN node_revision as nr ON nr.nid=n.nid AND nr.vid=n.vid
SET n.comment = 2, nr.comment = 2 WHERE n.type = 'notes';