So, I still don't get how this 1966 "black box" worked, but I take Bob Justman at his word that there was indeed some large, clumsy, expensive tehcnology available to have changed the pitch of Malachi Throne's voice--and, off the top of my head, probably Cloud Williams' in "The Omega Glory" and Lt. Mira Romaine's in "The Lights of Zetar."
Cloud William? No, his voice doesn't sound artificially deepened; he's just a natural bass. Heck, Ted Cassidy had a deeper voice than that.
The other major example of pitch changing in TOS would be Professor Crater in "The Man Trap," whose dialogue was slowed or pitched down for a few moments after he was phaser-stunned.