Antec Three Hundred Two

To the last question first, USB sticks have been discouraged as boot devices since the release of FreeNAS 9.3–with that release, the boot device became a live ZFS pool, resulting in USB sticks dying quite frequently. Some users have had good lifespans with them, but they die much faster than they used to. Thus, a SSD is going to be the better way to go. Yes, 128 GB is overkill, but it allows plenty of space for wear leveling, and they’re cheap.

Now, to the case. I don’t have any experience with it, but like you, I’d be concerned about cooling. Unlike you, I wouldn’t be confident they had it taken care of, but again, that’s more a gut feeling than anything else–when you’re stacking drives together like that, you need forced-air cooling. My preference for large numbers of drives is a used rack-mount chassis, generally from Supermicro; you can often even get them as complete servers for a pretty small cost delta. Here’s a nice clean-looking 2U, 12-bay chassis:

It comes with a SAS expander backplane, so a single SAS controller will handle all the bays without a problem. Dual redundant 920-watt “quiet” power supplies, too. But shipping makes it a more expensive proposition.

Something like this gives you a near-turnkey server:

Replace the RAID controller with a HBA, and you’re set with plenty of CPU and RAM for any reasonable use case.

This might be better yet. Again, you’d want a HBA rather than a RAID controller, but it’s the updated chassis with the two rear-mount 2.5" bays, and it has the SAS expander backplane the one above doesn’t. Just add CPU(s) and RAM:

All of those recommendations aside, if you decide to use the 302, keep an eye on disk temps. Free/TrueNAS will alert you if those go out of bounds, so make sure you have that set up.