When I was thinking about nanotechnology, the best explanation I could come up with was viral like particles. They can reproduce (with help of the host) and by altering the DNA code they can be programmed. The proteins they code for would allow them to be released or activated by certain nerve pulses which are controlled by our Nano Controlling Unit implanted below the cortex. If these bots leave the body they would not have enough energy (ATP) to do a lot; my theory was that Notum somehow replaces ATP. The NanoPrograms would be software running in the NCU that allows us to get the wanted nerve pulses without needing to do this complicated process 'manually'.
While some of this might apply to nanobots, certain lines from Prophet Without Honor make me assume that's not how Ragnär visioned nanobots and my explanation might be more suited for viralbots. Not that much is said about how nanobots work, but there two inconsistencies with my theory: 1. Nanobots are first generated in a Vacuum which is not to be expected if the bot was organic. 2. Nanobots use bio-electrical energy.
So yeah, I guess we have to assume nanobots are mechanical bots and not organic. The only issue is that viralbots/ organic nanobots look very realistic to me and are not so different from certain sections gene therapy. Mechanical nanobots by the year 2012 at the other hand sound just as likely as magic to me, but I'm not so much educated on this subject .
@Notcrattey: I guess the battlestations are close enough to Rubi-Ka to get some notum over there. If the notum diffusing through space is not enough, it should be possible to pump some notum in the cramped area's of a space station for nanotechnology to work properly. By the way: nano programs do work without notum, just less efficient and not outside the body .