Well, there is definitely space inside the computer for a second hard drive, although, without a cable to plug it in, I'm not sure what good it would do you.
Apple so far does not support SATA III in any of their devices, although that does not mean it will not work. Our experience has been hit-and-miss with SATA III in Apple products.
As far as using the second hard drive in RAID, It looks like you can set up RAID however you like. Check out [https://discussions.apple.com/thread/2213470?start=0&tstart=0|this thread]. Granted, they are talking about last year's Mac Mini, but since the two models are so similar, I'm sure you could probably do the same thing, especially since the SATA connectors on this [http://guide-images.ifixit.net/igi/TgOEa1o3oA3vcQSJ.huge|this years model] are the same as [http://guide-images.ifixit.net/igi/lDYQCkBEfXwDQSw4.huge|last years model].
As far as why not use Bluetooth for everything, thats gonna have to be a question best left to Apple. My guess is that they were trying to keep costs down, and they already have remotes and everything set up using IR and NFC, so they will continue to support those.
[guide|6131|Mac Mini Teardown]