The miners and PSU's can be on any side you want and also be packed together if desired. The fans are what do the cooling - not the exposed sides of the metal cases.
Personally, usually I never care about shut down but to prevent heat soak, just kill the pi or disconnect the data cable to the miner. It will go into idle mode with the fans running and you can then power down after they cool off.
Thanks - heat was not an issue with my single 741 proof-of-concept project (yes I ease into things). So when I expanded the project to 4 841s I assumed I would have (4miners X (0 heat issues) ) with the 841s. Definitely bad math.
Still hashing around 54THs - nice machines for sure.....