Can I pair two devices over Bluetooth without a need to confirm this in user interface, accept to pair this devices. Can I exchange some extra data over, for example NFC, an
Well, this should really be broken into 2 parts:
I'm not sure how you do it in Windows land, but in *nix land there are functions buried in the Bluez stack that let you receive notifications about when a new device appears, and send it the pairing code (clearly there have to be these functions: those are what the user interface use). Given sufficient time and experience I'm sure you could figure out how to write your own version of the Bluetooth Settings app that somehow:
All without having to pop up a user interface.
If you go ahead and write the code I'd LOVE to get my hands on it.