Layout does not take care of invisible links

Layered Digraph does not takes in account non-visible links, is there a way to force it to do so ?

Yes, it does ignore Links (or Nodes) that are not visible.

LayoutNetwork.addParts iterates over the given Parts. Only if Part.canLayout() is true will the Node or Link be included in the network as a vertex or edge.

Part.canLayout is defined as:

Part.prototype.canLayout = function() {
  if (!this.isLayoutPositioned) return false;
  if (!this.isVisible()) return false;
  // also consider whether this.layer.isTemporary
  var lay = this.layer;
  if (lay !== null && lay.isTemporary) return false;
  // link labels are always laid out by their Link, not by the Diagram or Group
  if (this instanceof Node) {
    var n = /** @type {Node} */ (this);
    if (n.isLinkLabel) return false;
  return true;