I should probably read up on RAID configurations and NAS setups, but I'm gonna learn how to OC my new computer soon so that might have to wait for now ^_^
WHS-2011 is the home-server Windows-version based on Win Server 2008 R2 -- loosely compatible with Win 7 in terms of drivers and essential features.
"AF" means "Advanced Format," which requires Win 7 and WHS-11 to "emulate" pre-AF 512-byte sector-size from a new AF sector-size of 4096. With Win 7 (AFIK) this was implemented in SP-1, as with WHS in updates, roll-ups etc. Win 8 should not have the "transitional" fixes precipitated by AF.
"Free space minimum to effectively defragment . . . " I'd say it would become more difficult with less and less free space, but I'd begin to worry with only 20% free space left -- thinking to move files to another location. Frankly, I try to keep at least 30 to 40% "free," or begin to consider migrating files with less than that. Someone else might be able to tell you a more robust "rule-of-thumb."
My understanding or explication may be imprecise, but there's no advantage to defragging SSDs, since there's no delay in reading from one fragment after another. Further, it degrades SSD by adding unnecessary writes to usage. Again, someone else can offer keener insight to this.
As for "striping" and "stripe-size:" You mentioned a desire to "mirror" disks, which would imply "RAID1". So "mirroring" is one approach to how two drives might be configured. "Striping" is the basis for RAID0. Files and data are broken up into chunks or stripes allocated equally between two physical disks. Thus, if you lose one drive in a RAID0 -- you lose it all (unless it had been backed up).
These new high-capacity HDDs are certainly not expensive, even after the "Tsunami-effect" that took place in the market a few years ago. So I can't try and tell someone that 9TB is a lot more disk capacity than you'd want in a workstation -- and that may reflect what "I think is necessary" anyway.
But you might begin to think how you'll back up your material to stave off disaster if a drive fails and becomes unrecoverable.
The other thing to think about is the power draw. I'm replacing all the boot-drives in our household workstations with SSDs (more expensive) with hopes of reducing our power consumption. I used to have a workstation with five HDDs running 24/7; other workstations with one and maybe two (RAID0) boot-volumes; and at least three disks running in my server. Now I have two SDDs and four HDDs in the server. I have a single HDD in my main workstation for DVR recordings -- two SSDs for boot volume and program -- and/or other data files.
A lot of my working files are stored for direct-access on the server -- which runs 24/7, and the server takes backup images of all the house workstations every night -- allowing for a bare-metal restore if a boot SSD or HDD fails on a Workstation.
You have a lot of options as to how you might configure those three drives. You could, for instance, make a 3-drive RAID0 (with the understandable risks) or a 3-drive RAID5 (incorporating the fail-safe features of RAID1 and the speed/capacity of RAID0).
Or -- you could configure your system BIOS for SATA "AHCI-mode" and partition/format the drives separately with separate labels. Or -- you could apply all the details in the first sentence here, and then create a "virtual drive" and drive-pool from the three disks -- with inexpensive drive-pooling software. Or -- the hardware alternative to the drive-pooling: a RAID BIOS option that simply makes the disks a "JBOD" or just-a-bunch-of-disks offering a single drive label.
I and others use StableBit Drive-Pool on our server systems, but the software developers have now assured that StableBit works for both Win 7 and Win 8 (as well as for most current/more-expensive server OS flavors. But StableBit is by no means the only drive-pooling software option.
One of the features of the drive-pooling software options: You can duplicate folders and files across more than one HDD so that nothing is lost (of those files and folders) if a single HDD goes south.
Take your time; do some reading; try and formulate a strategy that also includes some kind of workstation backup for this huge disk capacity.