So, first off, the method he's using is Fake:Japenese -> Spoken English translation -> chroniclers ciphers. that was his system.
So from what I gather you mean he translates it to English, then uses the pronunciations of the English words to convert it to the cypher. That is more sensible (and I'd commented on it being so from what I recall), than just using the fake:Japanese as spoken by an English speaker. The wording however suggested that he did the latter method.
First off, is the differences in phenomes between English to Japanese. English is considered to commonly has 40 phenomes. Japenese ahs closer to 100. so right of the bat that means it's not a 1-1 translation phenome wise.
While this is true, there is the issue that the chronicler's cypher would be a more intuitive writing system for a speaker of Japanese or presumably fake:Japanese. Additionally, English has only 26 letters, which is condensing things down even more, and pronunciation is based on letter groups (that are made up of an arbitrary number of letters, including 1 letter groups). This would be far more strange and hard to work out for a translator. Really, the idea that the graphemes correlate to phonetics is likely the starting assumption in a setting where that's how all the languages work. That said, there is something of an issue with this view.
So let's say your mythical coder does try and decipher Toru's book. First, he has to recognize it as phonetics.
The thing is, while that would be required if one wanted to work out how the writing maps to spoken English, there is no reason the code breakers would be interested in doing so. As far as they are aware there may not even be a spoken form, and the language exists purely as writing to encode messages or notes in. The thing they would be interested in, is linking meanings to the patterns of symbols written, which would require properly recognizing said patterns. The question then becomes one of if the Latin Alphabet or the Chronicler's Cypher is better at preventing proper recognition.
So, as far as pattern recognition goes, which is better? Well, on account of how spelling in English makes use of letter groups where various combinations of letters alter how it is pronounced, this means there would be far more repeating patterns of letters than using the Chronicler's Cypher where each phoneme is represented by a specific grapheme. This could result in misattribution of meaning to a pattern of characters that simply represent a sound rather than being a meaningful part of a word that etymological roots would link to other words containing said pattern (for instance "ight" occurs in both "night" and "right", but there is not a common meaning behind it that the first letter is modifying, compared to "ology" in "biology" and "archaeology" which is the "study of ____"). On the other hand, the fact that words are drawn from many different languages means that there are spellings taken from said different languages, thus allowing a difference in meaning between two portions that sound the same but have different origins to be more evident (as well as possibly making it easier to link to other words drawing on that same source for meaning and spelling). What is easier to deal with likely depends on the person, so this is a bit of a tossup as to which works better for keeping meanings secret.
Then there is the issue of how the two writing systems deal with homophones, homographs, and synonyms along with the
overlaps between them as seen. Looking at the venn diagram linked, the bottom section of synonym that does not overlap with the other two categories is unimportant for this, as is the middle section for identical words, as both of these sections would be handled equally by the two writing systems (more or less, aside from potential issues noted above). As pronunciation is unimportant except in how it impacts the spelling of words written with the Chronicler's Cypher the bottom two categories remaining each only important for the writing system that makes them different. Namely, different spellings for the same word in pronunciation and meaning only impacts code breaking attempts if the word is written in the Latin Alphabet, as they would be identical in Chronicler's Cypher, while words with different pronunciation but the same spelling and meaning would be the same in English, but different in the Chronicler's Cypher. As the meanings are the same, these categories are only helpful in ambiguity caused by the difference making it harder to recognize patterns of meaning. The fact that there are decent amounts of both would make it largely a wash, but I'd place it in favour of Chrinicler's Cypher if Toru decided to introduce the random usage of various dialects/accents into the mix (for instance spelling a word like it's pronounced with a Southern Drawl, vs a Brooklyn Accent, vs a British Accent, etc.), though this might make it harder for him to read it himself later.
Looking at the top portion of the venn diagram though, it's better for systems to share spellings to add ambiguity, as the meanings are different and and that throws off recognizing patterns. Homonyms are the same between the two writing systems, in that both will have different meanings but the same spelling, so neither is better or worse there. As for heterographs and heteronyms, the former favours the Chronicler's Cypher, where it will have the same spelling, while the latter favours the Latin alphabet where is will have the same spelling. The question is then which has more examples, and I can't say I'm entirely sure., though I'd expect it to be heterogaphs, as I can think of more off hand, but then I don't really notice heteronyms except if I'm thinking about the topic while using them. There are lists that can be found of
both categories, though I'm unsure of how complete they are as well as how common the words in them are. It also doesn't help if only one half is used (of course, it would be possible for Toru to intentionally make use of either category more than one might in normal usage of English). That said, it seems likely that there are more heterographs than heteroglyphs, so I'd tentatively put this in favour of Chronicler's Cypher for difficulty in translating, if only a bit.
Ultimately, either writing system would likely be rather difficult for the translator if they have no basis to work with, though the Latin Alphabet would likely be clearly harder if they were trying to work with knowledge of the spoken form. Without it though, there are prone to be more instances of overlapping spelling/different meaning in Chronicler's Cypher, and it's easier to introduce cases of different spelling/same meaning via dialect/accent compared to just finding synonyms which works for both writing systems. However, given how difficult either would be for a random code breaker to translate with no prior knowledge of English at all, and nothing in a known language to provide context, I'd personally lean toward using the Latin Alphabet, even if it might come out slightly behind, if only because it would make it far easier to read personally, and there really isn't any reason to be adverse to using the Latin Alphabet since no one knows it. Being able to read it at a glance without having to mentally stop to convert it from the Chronicler's Cypher to the pronounced form and from there working out what it means, along with not needing to do the reverse when recording information, would be both very convenient, and also allow the reading and writing of notes to be much faster and thus able to be stored more rapidly, reducing the chance of someone actually seeing it. This speed could also be handy if in the future he needs to record notes in the field.
That said, there isn't really a reason he couldn't make use of both in separate circumstances (for instance Chronicler's Cypher for his notes at home when he has plenty of time to deliberate upon them and there is no need to rush, and Latin Alphabet while in the field (or with information he'll need to read in the field) where speed is potentially important). This would even be helpful in that despite being the same language, from a cod breaker's view, they are two separate codes that would not be easy to link together provided he doesn't make a key for them somewhere. For best results, Toru would avoid using both in the same missive/writing to help keep them seeming distinct from each other. It would also mean that if he decided to re-record his top secret orders in English using the Latin Alphabet before destroying the original and heading out on his mission, if someone stole it they couldn't try cross referencing the writing with his journal that is written in English using the Chronicler's Cypher.
owrtho