Does Apple Mail prevent duplicates from being created in the same folder when copying/moving messages and how?
Not only does Mail not prevent the presence of duplicate messages (2 messages with identical headers and contents, including time stamps), but it (or iCloud) sometimes creates duplicates (buggy behavior). These can be hidden in Mail.app but you will see them in iCloud-Mail (via Safari) or with another mail client such as Outlook.
If you need to delete duplicates you may want to have a look as https://www.macworld.com/article/2046576/how-to-delete-duplicate-email-messages.html .