Odyssey is full of malaka in all shapes and forms. If I remember right, the Greeks in Origins used it but also used other awesome swear words such as koprophagos or metrokoites.
What is the reason we don’t hear these in Odyssey? Is it because they were really in vogue in the Hellenistic period but not so much in Classical Greece? Or it was purely an artistic decision and/or the fact that different studios worked on the games?
The selection of swear words in these games has nothing to do with history. The best evidence for this is the word malaka, which is a modern Greek curse word, and would have meant nothing to the Greeks of the Peloponnesian War. The other words you mention, metrokoites ("motherfucker") and koprophagos ("shit-eater") are known from Archaic and Classical sources and would indeed have been used in Classical Athens, along with other similarly vulgar terms.