http://eu.coolermaster.com/es/product/Detail/case/mid-tower-cm690-series/cm693.html will give you case pictures showing that the flow is OK. It is one of the PC cases I am using and it is acceptable. I am just an owner, without any interest in the C-M company.
Couple of points, for a future reference... The first is a general one, a NAS is a storage server. It really requires
nice environment: stable and clean power, absence of vibrations, stable temperature and humidity (and there are very specific good ranges for both of them). It is not a whim or some fad or conspiracy. It is the direct result of mass manufacturing of commodity electronic components. I have in my living room a quietly humming (the CPU fan needs to be replaced :D) NAS with more storage, than a medium size company had in all their hard drives at the turn of the century. Would I be able to take that server to the Sahara desert or Brazilian rainforest? A power generator, would not be enough. I would need to take a sizable fridge too, and mount my server inside. I do not know, maybe very soon wine cooler makers will merge with PC case makers, as there is a market to cool storage servers at home.
Particulars about Cooler Master 690 III. I think you can make it quiet enough to keep it in your living room :) :
Air flow is acceptable for up to 7 drives in the 3.5" cage, but I had replaced the front fan with two 14cm ones. Drives can only be properly secured on one sides (at least to my liking), securing the other side would require removal of a front fan

. I have replaced the rear fan and added a top fan. I have only 5 drives in the 3.5" cage, and one went up to the 5.25" cage, for you that might not be an option. I did that not only for cooling, but also because only the bottom of 3.5" cage is very sturdy. I am guessing that the top 4 positions in the 3.5 cage were designed and tested only for SSDs.
I am not using WD Green drives, but I did have 3TB ones under a load there (I was transferring data). With the room temperature of 23°C, one in the 5.25" cage that has no fan, was running at 28-31°C (idle 26-27°C). While WD Red 4TB was 1-2°C warmer under the same circumstances. I am using WD Black hard drives, since I am accessing the server via SSH and running various shell tasks. Yes, WD Blacks are fast and I can serve CIFS and do other things. No, it is not a recommended use of FreeNAS (to run shell commands). No, I would not recommend WD Black hard drives for FreeNAS for two simple reasons: they use way more power than Red or Green, and they do not have latching SATA connectors.;)
I had to remove the front grill filter, since it really impeded the air flow. I have a model without a window, but with room for a fan or two fans on the side. The window option is probably for hackers in Alaska
