Supposing a rotor machine of the 1940s or 50s, with 36 characters instead of 26. Would the encryption of the ten additional characters as the most frequent bigrams or trigrams weaken the code? What better use of these (or any) additional characters would there be?
What you essentially do is compressing the plaintext before encrypting it. If the rotor machine offers a secure encryption, it should be secure for any type of input, including the compressed one. There is, however, a caveat: The ciphertext leaks the length of the plaintext and if you compress the plaintext, you change its length and therefore change what is leaked. Depending on how the encryption is used, this can actually cause problems. See this question.