Hello,
is there a way to remove duplicates and check only the content?

For example, I have the following mails which are exactly the same, except their header fields X-UI-Filterresults and X-Bogosity.

If there is no built in method: Would it be enough to write a shell script which does the job? Or is there anything I have to consider (e.g. akonadi)
The mails are imap-mails available for offline use.

Thanks

Do you mean the existing remove duplicates isn't suited? If so, you may want to file a wishlist request on bugs.kde.org (with examples of your use case if possible).