The 'Save Sent Mail in the Sent Folder' function is designed to create extra copies of your sent message. But this does not mean that the mails are sent twice to the receiver and this function only creates extra copy and stores them on the server 'Sent Folder', in case the server refuses to store your sent mail in the folder.
How can I disable the function of creating duplicate copies?
This is a per account preference and you can enable/disable the function from Airmail Preferences > Accounts > [Select the account] as shown in the below screenshot:
When you have disabled this option you’ll no longer have the duplicated sent messages in your sent box.