I think this is more of a question of what kind of project or team you are working on, not one of experience in web development. Because it seems that you're suggesting beginners use Sails or Meteor (if focusing on JS), which are great and allow for rapid prototyping, but they and other 'high-level frameworks' that implement these methods for you tend to be very opinionated with important details of developing for the web abstracted away.
If you're a student or are serious about learning web development (and want to focus on developing in JS), it would make a lot of sense to dedicate your time to actually learning Node and Express, figuring out all of these hairy details and 'manually' implementing the items in Venantius' list.
Or don't figure out the hairy details, because many of his items have proven and documented solutions in the Node context, and learning how to properly use bcrypt and passport isn't too difficult. These libs are a good middle-ground between low-level details and something more out of the box.