Hi,
Since HikaShop 3.0, we've redone the display settings for the custom order fields.
So first, check that they are configured like you want and save them once.
If you don't see them in the emails but you have the email display setting activated in the fields and the fields are in the order details, it means that you have modified the emails in the System>Emails menu and that you have overrides from an old version.
In that case, delete the customization of the preload for these emails and redo the customization (if any in the preload) using the new version of the code and it should work.