Would the encryption of bigrams and trigrams weaken the code?
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.