Most of the Greek names/words in Assassin’s Creed Odyssey are pronounced following modern Greek conventions, not ancient Greek. So, IIRC, Euboea is pronounced EH-vee-a, except in those instances where it’s Latinized anyway.
Handling ancient Greek is always tricky. Every scholar usually has a disclaimer at the start of their book(s) in which they apologize for being inconsistent. For my PhD, for example, I figured sticking as close to the ancient Greek was the way to go (so my subtitle featured “Mykenaian” instead of “Mycenaean”), except in cases where this would be silly (e.g. Athens and not Athenai). Ugh. I’ve since gone back on this – because it tends to be confusing to those not in the know! – and stick with forms that are most common in the English language, which tends to be Latinized forms (so: Apollo, not Apollon, etc.). I am also ignoring differences between short (omicron, epsilon) and long vowels (omega, eta): in Apollon, the second O is long, for example.
Anyway, when it comes to pronouncing: there are certain rules that a Classicist is probably better able to answer. For the most part, koine Greek is used as the standard in scholarship, which is mostly based on Attic, but from the Hellenistic period. But already in the Hellenistic period, we can see, from misspellings etc., a move to “iotification”. If you listen to modern Greek, there’s a lot less variety when it comes to vowels/diphthongs, because a lot of sounds have been turned into “ee” (iota) sounds. Hence, “hoi polloi” doesn’t have the “oy” sounds anymore (oy, guv’nor!), but sounds like “hee pollee”. Other diphthongs have also become simplified, like alpha-iota now sounding like a short E: “kai” is now pronounced as “keh” (and if it’s in front of a vowel, as “kj” and connected to the following word).
But from what I remember from the game, they mostly stick to modern Greek. A lot the Greek that you hear when going through towns and villages, for example, is entirely modern. “Malaka” is a good example; as far as I know, it’s use as a curseword is purely modern usage. (Again, not a linguist. But as a point of interest: the word does derive from an ancient word, namely “malakos” – when Hector’s lifeless corpse is dragged into the Greek camp in the Iliad, the Greeks make fun of him and say that he is “soft”.)