It seems that the debugger doesn't show the __proto__ slot/property for objects that have a parent of Object.create(null) in their prototype chain.
window.onload = function() {
'use strict';
var parent = Object.create(null); // we can not see the __proto__ slot
// var parent = Object.create({}); // we can see the __proto__ slot
parent.x = [3];
parent.inc = function() { this.x[0] += 1; };
var self = Object.create(parent);
self.inc();
// correctly outputs 4 but we can't see the __proto__
// slot when debugging (by hovering the mouse over the variable self);
// the same is true about browsing the 'Local scope' and the console.dir() method
console.log(self.x[0]); // 4
};