Ticketing Notification Templates should only include custom attributes that have the Client Visible property flagged as True. Do the missing attributes have Client Visible set to False? If not, please let us know since you may have discovered a bug in the system.
The Client Visible setting is used to determine whether or not the attribute should be visible in the Client Portal. However, this value is not copied over when adding a custom attribute to a request form. Instead, request form field visibility is controlled by the field's Visible setting. This allows for custom attributes to be used on multiple request forms and have different visibility settings for each.
I hope this helps to explain why certain custom attributes are not included in ticket creation emails. Please let us know if there is anything else we can do for you.