Email clients (AppleMail, Outlook, Postbox and Thunderbird) don't care about duplicate emails at all. What can you do instead?
Each email has a unique identifier. There is a longer explanation on the blog what that is. So each mail client could handle duplicate emails.
You copy emails to another mailbox or you export some emails to mbox. But the original emails may not be fully deleted. The result is a mess of duplicate emails. ALWAYS.
And what about the new mail clients like AirMail, Spark or Unibox? The older mail clients have a huge amount of functionality for a reason. They support all styles of workflows. The newer mail clients support more narrow styles of workflows. But they don't really offer new and improved tools like handling duplicate emails.
The only way to deal with duplicate emails is to use Mail Archiver. The application fishes out duplicate emails automatically.
If you have a more complex workflow and you like to keep duplicate emails on purpose then you have to use the new feature "Archive duplicate emails in multiple mailboxes" in Mail Archiver 5.3. But there the way duplicate emails are kept is clearly defined so that you don't end up with a mess.