Well, shielded would be better, but I don't think ribbons here would be a real problem. It sure looks a lot tidier with the ribbons ! If really needed, you can use aluminiumtape to get better isolation between the stereo channels.
The Sub-D's : I would definately place them vertically instead of horizontally. That way there will be less mechanical stress on the pins.
The 5K consoles that I have seen did have ventilationslots, and also fans inside. Big chunky EBM Pabst, controlled by regulators located on the PSU distribution cards inside the console.
But even though there are "silent" fans available : all fans will get noisier after a year or 2, doesn't matter how expensive they are, or which superduper megasmooth ballbearings they use.
Slots on top and bottom, that's what I suggest. And ditch all the electronic parts that you don't use, for instance the TR/IR chips (85507). Also the lateralswitching for the routing isn't needed in your case, you can take these out as well. even though this won't be a drastical improvement, this has 3 advantages : decreases powerconsumption, decreases heatproduction, and there will be a better airflow between the sandwiched boards. win-win-win.