Fans at the end of either end of the tunnel would work in either arrangement. The horizontal version can fit in side a rack mount 19" wide I believe. The horizontal version would also less prone to heating I think given the density.
As BkkCoins mentioned, There needs to be more spacing on the front side of the boards. I am working on a stacking design with the boards laying flat, heatsinks facing each other, with standoffs to provide spacing.
Figure at minimum 12mm on the front of the board for clearance, double that if you want to use vertical pcie connectors. Keep in mind the wiring needed for the board, you don't want to design anything that will kink the wires or make them difficult to replace. I'll have some initial designs up in the next couple days.
For the SATA debate. I think it's a very bad idea to use SATA. As mentioned earlier, they aren't designed to pull that much power. Additionally, there is more waste from power supplies that are only going to be powering the boards. Most power from the PSU is on the 12v rails. The best density would be to daisy chain pcie connectors to each set of boards, using as much of the 12v rail as possible.
+1
Thanks for this Steamboat... the SATA idea is something for a 2 to 3 board configuration at best and what BKKCoins was suggesting is that it would have to be redesigned board for a later time. I will take your and BKKCoins design notes and look for off the shelf casing particularly something in the 4U variety as I want 512 chips Klego'ed in a horizontal fashion.