Hello,
I can add it to the history but can't get it sent to the customer.
If you are using a custom field to set your shipping tracking number, the best solution will be to directly edit the code of your emails to add that custom field through "Hikashop->System->Emails"
In a couple of the order sections I've attempted to 'Notify' but no emails are being sent.
HikaShop uses the standard joomla email sending capability. If you can't send emails in HikaShop, it means that joomla is not able to send emails either.
You should configure properly the joomla email options (in the joomla configuration page):
help.joomla.org/content/view/51/68/1/7/