If you've had a hardware failure of some sort, or you're just wanting to find the files of your templates for some other reason, then you can find your original template files in the Finder by following these steps:
Right click the template in the Design Chooser
Choose "Show in Finder"
If Mail Designer 2 isn't installed on your Mac, you will find your templates here:
Mail Designer 2 Standard
~/Library/Containers/com.equinux.MailDesignerStandard2/Data/Library/Application Support/Mail Designer
Mail Designer Pro 2 (version 2.6) and Mail Designer Pro 3
~/Library/Group Containers/CPXNXN488S.Mail Designer/Documents/Pro
For previous versions of Mail Designer Pro 2 (version 2.5.5)
~/Library/Containers/com.equinux.MailDesignerPro2/Data/Library/Application Support/Mail Designer/Documents
In the Mail Designer folder, you will find a folder called "Document". Follow the path in this folder to find your custom categories and there your templates.
If you're searching through Time Machine you will need to follow this path of folders manually. However if you're simply looking in Finder normally then you can go to the top menu bar and select 'Go > Go to Folder'. Copy and paste the path above and hit enter.