As a U.S. citizen, I think part of the reason that languages are hand-waved is because linguistic flexibility is uncommon in this country, and this is where D&D is based for all intents and purposes. For most folks, learning a new language is an unnecessary chore. Many folks haven't had the mix of entertainment and frustration that come from trying to order from a menu when you aren't fluent in the local tongue.
I think this matters because if a group is comfortable with multiple languages, you can mix things up a bit. Instead of
comprehend languages, maybe it makes more sense to have a spell that works like Farscape translator microbes or Hitchhiker's Guide babelfish, and another set of spells for reading different languages. One is an interpreter, the other gives you temporary knowledge.
The quasi-telepathic translator would actually make spoken code phrases ineffective, as the
intent would be translated. Written ciphers, however, would at best translate into gibberish with the second spell.
Here is how you could break it down:
Comprehend Languages: Translates the intended meaning behind any spoken speech. It does not allow you to speak the language, though you can cast the spell again on the other participant in the conversation. It does not allow you to understand recorded text, such as that relayed by a
magic mouth. It will allow you to understand pass phrases, such as "the fish swims upstream," as meaning things like "I am a member of the thieves' guild." Anything that foils telepathy will foil this spell, too. You gain no skill at reading any language.
Language Savant: This spell allows you to learn a language after eight hours of normal interaction with users of the language. You can speak it and read it at a colloquial level for as long as you continue to use it for at least an hour a day. The knowledge fades with disuse after one week.
Learn French*: You gain the ability, for the duration of the spell, to speak and read a single language with great skill. You can read complicated texts, including treatises on complex magical or scientific topics. This will not break ciphers, but it will allow you to avoid any languages penalties while attempting to break them.
*Pick whatever fantasy language you want. I used French as a placeholder.
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So, if your FR character runs into somebody from ancient Netheril, comprehend languages allows them to understand what is being said, but not to speak back. If they run into a community of ancient Netherese, they can pick up the language for casual use quickly with Language Savant. If they run into an ancient Netherese cipher, they can use Learn Netherese in order to have at least a basic chance of breaking the cipher. Actually breaking the cipher magically should require divinations with higher (or lower) powers.