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While watching the movie the Martian, a question arose regarding the name Ares:

Greek Gods were metaphrased into Latin when Romans took over. Ares (from the Greek Άρης) was now named Mars, and so on. And, as such NASA uses the name Ares for their mission to Mars.

They also have a spacecraft named Hermes an import of Ερμής. By this convention, shouldn't it be Hares then instead of Ares, since both start with a vowel, followed by a consonant (character r)?

'A' might be an exception or something, yet, I remembered Hagia Sophia (in Constantinopolis), from the greek Αγιά Σοφία . This follows the same convention as Hermes, rather than that of Ares. Similarly, we have the name Hades.

Why is there variation in this convention?

Hermes and Ares are reasonable representations in the Latin alphabet of the sounds of the Greek names. The /h/ sound is absent from classical Greek spellings of words which contained it (like Hermes) because the Attic Greek alphabet did not have a distinct character for it—the character ‹H› was used for eta ('long e', contrasting with epsilon, 'short e'). Starting in the Hellenistic period the presence or absence of /h/ was indicated by diacritic marks, the 'rough' and 'smooth breathing' signs.

The /h/ sound was subsequently lost in Greek.

I’m afraid you are labouring under a misapprehension. Mars is not the Latin for Ares with an aspirated first letter. It is derived from the Oscan Mavors. He was the god of war, like Ares, but he was also supposed to be the father of Romulus and Remus.

Many of the stories about Ares and other Greek Gods were adopted into the Roman cannon.

But the names were not all the same. So the Roman opposite number to ΕΡΜΗΣ was not HERMES but MERCVRIVS (Mercury) - the V representing a ‘u’ as in put.

Others have already pointed out that the initial epsilon of Greek Ερμης was aspirated: Hence the imported H.

In modern Greek, vowels are not aspirated. So what in ancient Greek would have been Hodos Hermou (οδός Ερμού) or Hermès Street is now pronounced Odhos Ermou with no ‘h’ but an aspirated delta, pronounced as in ‘that’.