Hi,
What do you see when you edit the order in the HikaShop backend ?
You should have the order custom field in the section "Additional information".
You can also generate a preview of the email using the button "e-mail" in the toolbar.
I made a test in my local websites and when the order custom field is filled, I see correctly the value in the generated email (using the backend "e-mail" button).
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.