I don't really see how you'd practically use nanotechnology in agroforestry design? Or why? As I see it, a lot of the appeal of permaculture is that it uses tools that can be understood by anyone, which makes self-reliance and resilience possible. None of us will ever be able to make a nano-bot from scratch without the aid of all of the industrial system. If we start using (and eventually depending on) the most advanced products of that system, we're effectively at its mercy.
Of course, I can't build a computer from scratch, and still I use them. However, if all computers were to break down tomorrow, it wouldn't affect my ability to garden. If, on the other hand, I'd taught myself to garden with lots of computerised aids, and convinced myself that was the only way, I might be in trouble if they were no longer available.
In short, I don't see the benefit of nanotech in permaculture, I think incorporating it might be very destructive, and I'd rather put my trust in a system that's evolved over 3.8 billion years than in one which might possibly be invented ten years from now.