I understand that the general sentiment for this article seems to be dismissive but I want to share this awesome University of Vermont lecture series/course. It's related to forecasting mathematics and includes an introduction to fractal geometry which I haven't seen much of elsewhere.
According to his initial explanation - "In a peer to peer botnet, bots which can receive incoming connections act as servers (called supernodes)."
So in some cases the only requirement for a node to be a supernode is that it can receive incoming connections. I take this to mean that any computer that is 1. infected with the botnet program, 2. can receive incoming connections, becomes a supernode. Under those circumstances there's no need to reverse engineer the botnet program, all you have to do is set up a vulnerable computer, allow it to be compromised and infected becoming a supernode; then monitor the traffic of incoming connections.
He later mentions that supernodes can be filtered based on "age, online time, latency, or trust." This tells me that certain botnets do have a level of trust that is defined in each peer list.
I believe your last question refers to the concept of sinkholing or blackholing. These methods have been used by the FBI to take down botnets through DNS hijacking, I think.
Yes to your first question, no to your second. He goes on to explain that, "In order to map all workers, we’d need to set up multiple supernodes across the botnet which log incoming connections (obviously every worker doesn’t connect to every supernode at the same time, so it’s important that our supernodes have a stronger presence in the botnet)."
From what I understand the process is:
1. Write a program to pretend to be a compromised peer requesting a connection to a Supernode in order to obtain a peer list of other Supernodes.
2. Recursively crawl for existing Supernodes + the list of Supernode IPs. Store all addresses found.
3. Set up one or more Supernodes and 'infiltrate' the peer list of already established Supernodes. Log incoming connections from Workers.
"In computer networking, a hop is one portion of the path between source and destination. Data packets pass through routers and gateways on the way. Each time packets are passed to the next device, a hop occurs."
https://youtu.be/Lr3qrB6dPCM