First of all, sorry for the slow reply. I thought I'd setup an automatic email notification but apparently not.
At the end of the day, a system is only as quiet as what you put into it. If you want a system with that many hard drives to be quiet, I think your first concern should be how and where the drives are mounted. Sturdy metal drive cage and soft decoupled mounts is what to look for there.
Basically, if the drive mount/sleds are bad then the entire case can vibrate audibly. I actually had that problem in an Silverstone Raven RV02-e which disappeared when I moved the rotating media to one of these:http://www.silverstonetek.com/product.php?pid=249
3x 3.5" drives in 3x 5.25" bays isn't the most efficient way to mount drives, but the grommets on that one are very big and soft. I'd definitely recommend that part if you need some extra drive slots.
Also, storing unused HDD's inside the case IMO would be counter productive for airflow reasons. If you need some drives for intermittent use then I'd look at USB enclosures for them or consolidating on to fewer, larger drives.
I know that the DS1 stuffed full of drives may not be the ideal solution but I'm only running a Celeron G540, so cooling shouldn't be too demanding and, to be honest, the DS1 was the best solution I could find. Ideally I'd have a NAS with plenty of drive bays but that'd defeat the purpose of my build. I want to learn how to create a NAS/home server using the hardware I've already got... that and the prices of large NAS enclosures are really high to my eyes. As for buying enclosures for the various homeless drives, again I think the compromise of having drives stuffed into the DS1 outweighs the expensive of a new, quiet case with fewer 3.5" bays + the HDD enclosures for the drives that I can't fit in the case but that assumes that they aren't a major obstacle to cooling my beastly G540. Which brings me on to my next point...
I have a 14-drive system in Nanoxia DS1 (+1 SSD). Case itself is good, fans are relatively quiet, but the biggest noise maker will be the drives. With RED and Green drives it could be heard in a silent room or at night, but i could sleep in same room, so it wasn't bad. The only real alternative i see to DS1 is DS6 :http://www.nanoxia-world.com/product/1/ ... Silence+6+
10+3 bays in default, and i would say you can easily add 6-8 more plus something in the four 5.25" bays.
The DS6 is just too big. I've already got one oversized tower in my room and I really don't have space for another... the DS1 is marginal as it is but there's nothing else out there (short of an exorbitantly expensive NAS enclosure) that holds the same number of drive without being huge.
It's decision time. The DS1 has been out of stock for months at my selected retailer but it'll finally be back in stock soon.