[SalesForce] In HTML Email Template lookup field showing Name field of the related lookup object, how can I get Id instead

From what I remember standard emails (= non-Visualforce ones) will give you hard time when you want to use more than one dot to go "up".

I'm aware of only 2 workarounds you have mentioned:

• a helper formula field (type = URL maybe? so it's at least a bit reusable); I've created "Case Contact's Phone" etc that way in the past
• craft the URL by hand using the trick described in Detail page link under email template

There is an Idea for this: use cross-object merge fields in email templates that, as of December 2015, is under consideration. Vote it up!

Since your schema is:

Contact          Disease
   |                |
   |                |
   |                v
   ---------->  Patient

OPTION 1

You will need to send the Email on Patient and where Patient has two custom formula fields:

Patient Contact Email - defined as Contact__r.email
Patient Disease - defined as Disease__r.name

OPTION 2

Create a new custom object called Email Proxy. Update that with all the fields you need to send the email (recipient (as field of type Email), disease name, patient name). Add a field called "Is ready to send". Point the template at the email proxy object

Use workflows or process builder to send the email (because "is ready to send" is true. Reset this field to false after workflow/process executes