The reason for copying an email to a different folder is that it is important. You do not want to loose it, and you want to be able to find it there.
It is wrong to assume that a user will notice that these emails are missing and should look for them elsewhere. 
Say you have folder for a court case, and you copy emails there relevant for the court case. How can you ever know after a restore that a few email are missing from the folder, and which ones.

I think it is bad this email is currently 'lost'. I rather have an option in dovecot that disables this hidden 'deduplication' feature. I think this should be the default setting also.

This current deduplication feature also is hazardous because if this one copy of the email gets corrupted on the storage, you have no copies left. That is exactly the opposite of what user wants to accomplish with creating a copy.

Feature request: disable this automatic linking of emails between mailboxes.
Feature request: set this as a default.