I've got an academic curiosity regarding some of the old Japanese naval codes used during World War II specifically. I'm wondering if any of the codebooks from this era have been made available, or if they are still protected materials?
Yes, a good bunch of Japanese naval codebooks and related documents from WWII are available.
You might want to contact the National Archives and Records Administration (NARA) for that, as they hold the related NSA documents which have been declassified.
The “Declassified Documents Released to NARA” list at the NSA website points (among other things) to ample Japanese naval codebooks (random example: “NR 4037, ZEMA150, 45441A, 19440218, CODES AND CIPHERS: JAPAN JN-155 CODEBOOK”) as well as dozens of similar documents containing Japanese naval codebooks, naval call-signs, naval communications indicators, brevity codes, etc.
Looking at The Freedom of Information Act, it shouldn’t pose a big problem to get a copy of those documents to satisfy your academic curiosity.