The implicit assumption behind the issues raised here seems to be that closing is a form of removing, hiding, or destroying something we do not want. I would like to suggest that closing, on the contrary, is an act that adds information and value to our site. To understand this, bear in mind that the threads associated with closed questions remain visible and searchable.
Pointing to an off-topic as a duplicate is rare, but it is not inconsistent. Although questions can officially be closed for only one reason, often several apply. Moreover, off-topic threads frequently collect comments (and, on occasion, answers). Linking to such threads is informative.
Closing duplicates of unanswered questions makes perfect sense. When the same question appears in two or more places, then for the purpose of deciding whether they are duplicates it does not matter whether neither has an answer. We want to link them so that all the answers (and, hopefully) comments appear together in a conveniently read, easily searched way.
The proposed solution--do not mark unanswered questions as duplicates--would only cause unanswerable questions to proliferate and degrade our site. As far as I can see, the only reasonable alternative is to delete duplicate questions. It is rare for moderators to do that, because duplicates are almost never phrased exactly the same way: they may contain different key words, for instance. In many cases it might not be evident to a neophyte that two questions are really duplicates, because recognizing that might require understanding the meanings of related technical words or of making a simple mathematical transformation. The act of linking a question to a duplicate embodies such an insight and itself creates meaning. This adds value to our site, whether or not either question currently has an answer.
There is a problem, however. It lies with the system's stock phrase, automatically applied when a duplicate is closed:
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.
This obviously is not true when the duplicate does not have an answer--but there is no way anyone here on CV can modify this text to make it more accurate.