Anyone could be confused by this, especially in the case of the Zimmermann telegram.
Codebooks come in three flavors: one-part, two-part, and hybrid. You described a one-part codebook. These are somewhat vulnerable to guessing because they are alphabetical for both plaintext and ciphertext. For example, using English, if you know that 22667 stands for Vienna, then 24556 must be something that starts with W, X, Y, or Z. Two-part codebooks have, according to Merriam-Webster, “an encoding part listing the plaintext segments in alphabetical and logical order each with its code group or groups assigned at random and a decoding part listing in alphabetical or numerical order the code groups with their plaintext equivalents.” They are less vulnerable to guessing.
Since the one-part codebooks were somewhat vulnerable to cryptanalysis, super-encryption was often employed.
In World War 1, diplomatic and field army communications were often super-encrypted at the time of transmission with a substitution table or an additive-- which usually did very little good, especially for the Germans.
On page 252 of the 1967 edition (Macmillan Company) of The Codebreakers, David Kahn goes into detail about how super-encryption was done:
“...super-encipherment was a form of substitution; the 'alphabet' was
an ordinary scale of numbers. This method added a keynumber, called an
'additive,' to the original codenumber, called the 'plain code' or
'placode.' The sum constituted the final cryptogram...”
During World War 1, the German embassy in Washington D.C. received what would be called the Zimmermann telegram, which had been encoded with German diplomatic code 0075. Relatively new, this codebook had been in use since mid-1916.  They forwarded the telegram to the German legation in Mexico City by simply re-encoding the plaintext they had just resolved from code 0075. The problem would be that they chose an old German diplomatic code, 13040, to re-encode the telegram—just as the British thought they would (Dooley, p. 92). 13040 had been around since 1907.  Over the years, the British had broken 13040, which was a one-part/two-part hybrid, the old-fashioned way: painstaking effort. 
The Germans in Mexico City did not have 0075, but they did have the much weaker 13040. In short, a decoded ciphertext was re-encoded with another codebook, one that had been broken. Mysteriously, there was no super-encryption—not that this would have helped because using additives prior to transmission did not tend to slow down the British, and in this case, the Brits already had enough plaintext to understand the message, especially the part about unrestricted submarine warfare against the United States.  Barbara Tuchman, in her book about the Zimmermann telegram, writes:
"Generally, although not always, when the Germans used code they
wrapped it inside an extra covering of cipher; that is, they
enciphered the code. The key to the encipherment they changed
frequently—as time went on, every twenty-four hours. But, being
orderly Germans, they changed it according to an orderly system which,
once solved by the cryptanalysis of Room 40, could be solved again
each time by progressing according to a constant pattern. For some
reason still obscure, the Zimmermann telegram, when it was sent, was
not put in enciphered code." 
At the time the message was sent from Berlin—16 January, 1917--the British had only partially broken 0075. But they had been very hard at work. They later came up with a romantic story--about a suitcase from Iran containing Code Book 13040 showing up in England —to cover their collection and cryptanalysis efforts, both of which were intense. They had in fact been spying on American diplomatic cables, sent over copper wire, thanks to their relay station in Cornwall, where they intercepted the Zimmerman Telegram and broke enough of it to learn its meaning. The Germans had actually sent their cable from the U.S. embassy in Berlin for forwarding.
The British then bribed one of the staff at the relevant telegraphy station in Mexico to get a copy of the 13040-encrypted ciphertext that Western Union had received. After that they invented a cover story to hide their cable-telegraphy collection against the United States, and conceal their significant cryptanalysis capabilities, they lied and said that they had stolen the deciphered telegram in Mexico.
David Kahn also goes into detail about how super-encryption was done over Morse telegraphy prior to, and throughout, World War 1. He also mentions how German super-encryption was first solved by the Allies, on 13 October, 1914, by Charles Rotter.  Super-encryption ended up being relatively unimportant because it tended to be weak, but cryptanalysis made a name for itself.
John F. Dooley wrote a book dedicated to World War 1 cryptography: Codes, Ciphers, and Spies: Tales of Military Intelligence in World War 1. He talks about how the Germans shifted from ciphers to codes in early 1917, and how the Geheimklappe enciphering and deciphering tables were used to super-encrypt codebook traffic. On page 66 he goes into detail about how it was done in the early part of 1918. They would substitute the first two digits of each three-digit plaintext word by using the Geheimklappe.
Traffic looked like this:
AN v X2 (Souilly 0040) 0025 CHI-13
845 422 373 792 240 245 068 652 781 etc. (Dooley 2016, p.66)
Concerning World War I, we should distinguish between German diplomatic traffic and that of the field armies. The ADFGX and ADFGVX ciphers were used on the ground, also transmitted in Morse, but over crystal set radio and not superencrypted. Both sides used Low Wave and Medium Wave bands for their radio telegraphy because, prior to 1920, frequencies over 2 MHz were though to be useless. 
ADFGX came out on 5 March, 1918, close to the end of the war; it was later to become ADFGVX, on 1 June, 1918.  Interestingly, the French broke ADFGVX in 26 hours. (Kahn 1967, pp. 344-345). Both used a Polybius Square with a mixed alphabet for fractionation (biliteral), followed by a single columnar transposition—no superencryption. But other encryption systems for radio such as the American Trench Code used codewords that were designed to be superenciphered – using substitution (Dooley 2018, p. 97).
 Dooley, John F. 2018. History of Cryptography and Cryptanalysis, p. 90.
 Gathen, Joachim von zur. 2007. Zimmermann telegram: the original draft. Cryptologia 31 (1):
 Boghardt, Thomas. 2012. The Zimmermann Telegram: Intelligence, Diplomacy, and America’s
Entry into World War I. Annapolis: Naval Institute Press. p.84. Interestingly, he disagrees with Kahn about the superencipherment of the telegram. See p. 253.
 John Dooley says, “The British had worked out most of the code groups in 13040, to the point that they could easily remove the superencipherment and decode any German messages in the older code...”, p. 90.
 Tuchman, Barbara. 2014. The Zimmerman Telegram. Chapter 1. This book is a tremendously good read.
 David Kahn says that the 0075 message was probably superenciphered, but the 13040 message was not. Kahn, David. 1967. The Codebreakers. p. 293.
 Their cover stories lasted for decades, and this is one source of the confusion about the Zimmermann Telegram. See Freeman, Peter. 2006. The Zimmermann Telegram revisited: a reconciliation of the primary sources, in Cryptologia 30 (2): 98–150.
 Kahn, David. 1967. The Codebreakers. p. 268.
 Oleg Golovin, Aguilar Hardon, Nikolai Chistyakov, Wolfgang Schwarz. Radio
communications. Moscow. 2012. Hotline – Telecom, p. 25-40.
 Dooley, John F. 2016. Springer. Codes, Ciphers, and Spies: Tales of Military Intelligence in World War 1. pp. 83,87.