I have found that using a ubuntu base AMI and salt ( http://saltstack.com/community.html ) makes things much easier to manage. His suggestion of having node.js and nginx baked into the AMI is a big pain when you need to upgrade node.js or nginx (hello security update!). Using something like salt (or puppet or chef) would make this much easier. But in general, I agree with the article.
Granted node and nginx don't take long to run an update on. But the more you keep piling on updates the slower your true "time to ready" increases. And that can take a while from ec2 launch to ELB registration.
Why not have best of both and use puppet/chef to create your AMI anytime they require a security update?