So, a very useful tool is to look at the "linked" questions. How does this work? I think it should act as a sort of connected component. So that when you look for the questions linked to $A$ you don't only get the questions that where directly closed as being duplicates of $A$, but also any other questions that may be involved with $A$ in some way. Does it works like that right now?
As far as I know, it does not work this way.
According to the tag-info (maybe somebody can find a more official source):
The "Linked Questions" sidebar is a user-generated list of related questions shown when viewing a question. Its content comes from questions that users have linked in the question, their answers, or in comments.
I will add that both questions linked in a particular post and questions linking to this post are added to the list. See also here. (You may notice that your question is now in the list of linked questions for that post.)
I do not think that such feature would be useful. Just take, as an example, a question, which asks for a proof of some frequently used fact. This question might be linked in many other answers as a reference for an auxiliary result. All questions, where an answerer used this post as a reference, would be linked to each other.
No. I just tested it. I took a random question with a linked question and posted it in an now deleted comment. Post $B$ did show up, but post $C$ didn't.
However, I think that this could be very useful. I think it would be better if you posted this at meta.stackexchange.com.