Shiptheory can trigger an email to be sent to your customer using your Magento email template through the Order Comments found on each order. To Enable/Disable this functionality, use the Notification Options from the Magento setup page within your Shiptheory account as shown below.

I have disabled email notification but order comments are still being sent. Why?

Shiptheory will only email your customers from Magento if the above option is set to Yes. Although you may still notice order comments are updated by Shiptheory, only comments with a green tick will have been sent to the customer.

In the below example, only the second order comment has been emailed to the customer, as indicated by the green tick next to the word Notified.

Order Comments are not ticked, but I'm still getting the email. Why?

In Magento, under System -> Configuration -> Sales Emails -> Order Comments, if you have "Send Order Comment Email Copy To" email set, as shown below, you will be emailed every order comment, regardless of which emails are sent to your customer. This is default Magento behaviour. You customer is not receiving all of the order comments that you are receiving.