Is it is good to mark a question as Duplicate with reference of negative score question?
The quality of the question is irrelevant to whether or not the post is a duplicate. The point of duplicates is to point a user to answers that should address his/her problem.
A question which does not have answer, should be refer for marking Duplicate for other question?
This is not permitted. In order to close a question as a duplicate of another question, it must have an upvoted or accepted answer. The only exception is when the OP of both questions is the same. The reason is that it is not uncommon for someone to repost a question that didn't get any answers or was closed or heavily downvoted, so the ability to close those types of duplicates is necessary to keep the site clean.
Meta sites are also exempt from the "requiring an answer" rule. The reason for this exemption is to deal with frequent repeatedly asked feature-requests and discussions, and also bug reports in general. It is not uncommon for Meta questions to never get an answer (for various reasons), so if the requirement was in force, it would be much more difficult to close questions. Having multiple posts with the same topic only splits the discussion and makes it more difficult for the SE team to track problems and issues.
Is there any Standard or FAQ for Duplicate question marking?
Not really, at least not from the perspective you are asking for. This is because interpretation of the close reasons can vary based on the individual, so there is no one true guide. For example, some people think that the questions need to be exact duplicates before it should be closed. Others feel that as long as the answers address the problem and the questions are very similar, then it is good enough.
What should do if we have found such any scenario?
I think this is pretty much addressed in the response to your other questions, but in short you do nothing different than you would do for any duplicate question.
Now you ask what if none of the answers on a duplicate question doesn't address then problem, is it still a duplicate. That is somewhat of a gray area as everyone is going to intepret that differently, but in general, the close message on duplicates covers this:
marked as duplicate by <5 random people> 2 hours ago
This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.
So if the answers are not sufficient, you are invited to ask a new question. What this means is if this is your question and the duplicate target question has answers that don't address your problem, you need to address why the question is not a duplicate by editing that explanation into your question. Such an edit would put the question into the reopen queue so other 3K users can vote to reopen it if they feel the explanation accurate covers why it isn't a duplicate.