@Hazoss
If you have the EHD bearing Time Machine attached; and you followed Moderator Slydude's clear advice in post #97 as you seem to have done — and you've seen the Mail folders and, for testing purposes, restored an email or Mailbox, then case closed. Time Machine has all your emails.
In fact, as you have told us that you made no exclusions when you instituted Time Machine, your emails would definitely have been stored.
If you want double security, get another EHD and do one of two things:
Assuming you are running OS X Mavericks, Yosemite or El Capitan, you can add the EHD and create a second Time Machine backup (BU). The first BU will take for ever, but all future BUs will be incremental. Then you will have 2 Time Machines with everything stored. I have that arrangement.
The second option with the new EHD, is to purchase cloning software (Carbon Copy Cloner and SuperDuper! are the leaders) and clone your iMac's HDD. However, no offence intended I promise you; but I got the distinct impression that you were tending to shy away from cloning things either because of expense or assumed complexity. That is why I suggested the 2 Time Machines option.
By the way, the Time Machine EHD (or Drives, if you go for two) should ideally remain permanently attached to your iMac so that they are left to do their job; namely, BU on the hour seamlessly in the background.
Do you feel more reassured now that Mail is backed up? And how to achieve a second Time Machine BU as well if you're worried?
Ian