Why do you think you see the layers loading? If the layers pane does not show any layers, then there are no layers in the document.
Because you can see the document loading in layers, not all at once. Also, it says it is flattening the image when sent to the printer.
What you see is a complicated file loading. PDF layers, if there are any, don't load any differently. PDF layers are nothing like Photoshop layers.
Flattening when printing is nothing to do with layers, it's flattening transparency.
So, there are almost certainly no layers, though the layers palette can be deliberately set up empty. Most PDFs don't have layers.
Thank you for clearing that up for men.