If you run external drives with stock factory enclosures they will most likely overheat and die. Take them out of the enclosure at a minimum.
Yes. Thanks for this helpful advice mate. With this in mind, I would leave the external HDDs exposed out in the open without the use of the case, in order to maximize air flow and coolness. I'm saving a lot of money in order to buy a couple of hard drives and some gear necessary to get started with this thing. It will be pretty interesting how everything will work with the Raspberry Pi 3 once I finish the setup.
The Synology DiskStation DS414Slim 4-Bay 2.5" Diskless 2xGbE NAS has really brought my attention. It is perfect for those spare 2.5 laptop hdds I have lying around. You can check it out here:
http://www.mln.com.au/product/?itemID=5686