Why nodes are stdClass? My question is a little bit vague. Why do we use stdClass(es) to represent objects in Drupal 7? is there a practical use to it ? Why not just using arrays ?
Generally speaking, objects are used for storing structured data and arrays for lists or collections.
It even logically makes more sense. Node is an object with properties; it's not an array of properties.

See this answer posted on SO as an example.