Actually, the design does have a heat evacuation wind tunnel at each layer. The upper section of each tray has an isolated heat channel that collects hot air as it's drawn up from the radiator fins where it's blown out in exhaust.
First of all, The individual board fans are much too close to the tray above it; depending on what kind of fan you use, you could be losing as much as 50% airflow from that alone, while generating more noise too. Just try it, take some case fan, hold a paper 10 cm above it, and see (and hear) what happens.
Also most the exhaust (side) fans are actually fighting with the board fans; I assume they suck air out, but they do so below the board fans (ie, hot air, which is good) but also above those fans, ie, they also suck out relatively cool air and while doing so fight the individual board fans, further depriving them from airflow.
Now Im not saying it wont work, they may run cool as cucumbers, but if they do, you could have achieved the same or better with less fans and noise using a better design IMO. And to be honest, going by the results of the singles which seem to overheat in anything but an airconditioned DC, I cant say Im confident.
You guys seem to be quite competent engineers in your areas of expertise making awesome products, but for system/cooling design, Id really consider getting some outside help, or at least inspiration from other designs.