The answer to the original question deserves a better treatment, as it gets seemingly less attention than the answer for the duplicate.
I agree. That answer seems to me to have more value than any of the answers to that question. It's the only answer to either of those questions that I've upvoted.
However, that answer does not really address the question of what the a stands for in ls -a. Perhaps the question is not really a duplicate at all.
Unfortunately, short, easy-to-read answers tend to get disproportionately upvoted, while long, comprehensive answers tend to be undervalued.
However, those answers (to the duplicate) have independent value, and don't duplicate information found in the answer to the original post.
If there was no question, there would be no answer, so blaming the asker but still awarding the answerer seems kind of strange.
Again I broadly agree with you. I don't think there was anything wrong with that question. The man page for ls does not give the answer to it, so arguing that the question is downvoteable on the basis that it "lacks research" is dubious. However, downvoting it because it's not a very interesting question seems reasonable to me. Maybe that's what the downvoters felt.
In general, asking a duplicate question might (dubiously, in my opinion) be taken to indicate a lack of research (why didn't you find this other question that has the answer already?!) but we all know the internal search... doesn't always produce helpful results, and research is very hard when you know nothing.
I try to vote based mainly on the usefulness of the post. Duplicate questions are sometimes very useful because they have valuable answers, or somewhat useful as signposts, and sometimes they do not add anything useful to the original post. This question, even if it should be considered a duplicate, is arguably somewhat useful because its answers tell us something that is not well explained by the answers to the target post, and arguably not useful, because the question of what the a in ls -a stands for is a boring question - "why did the developer of this program make this decision?"
Finally, the title of your question Do good quality answers on duplicate questions deserve reputation? suggests that you are thinking about the reputation effect of voting, which is far less important, imho, than the peer-review effect of voting. Voting is not primarily to reward the poster with reputation or penalise them by reducing their reputation, but to indicate to site users how useful a post is. So my answer is that useful posts deserve upvotes, and that may certainly apply to good quality answers to duplicate questions.