Missing Mail.app in Finder, but exists in /Applications folder
Thanks to the hint from @Zero, there is a way to Hide and Show individual files, including applications from Finder by using Terminal. 

To Show individual files:

sudo chflags nohidden Mail.app/


To Hide individual files:

sudo chflags hidden Mail.app/


Depending upon the file, you may not need to use sudo, but it won't hurt in any case (other than needing to type in a password).

Disclaimer: I found the key to my answer mentioned in a comment here: https://apple.stackexchange.com/a/65175/84492