Hmm... Interesting theory, but I'm not fully sure. The regions up to Unova are all based on somewhere in Japan (Kanto, Kantō, etc), and the franchise is more popular in Japan, but they could have been trying to appeal to a wider audience, just like the case in Unova, and the upcoming X and Y region, based off of Europe. I am trying to think that this "Shipwreck" and the shape of Sootopolis City are mere coincidences, but anything is possible. Look at Orre, for example. This is a region that is EXPLICITLY based off of Arizona, in the United States. The folks at Gamefreak probably wanted to broaden their venues, and create this desert, America-Based region. If Hoenn were like Greece, this would also hold true (Just so we're on the same page here, Orre was revealed as inspired by Arizona in an interview).
Still, Hoenn has its similarities to Greece. The myths of Hoenn could have loosely been inspired by the Gods of Greek mythology, and I personally think that some music included in RSE has Greek roots, like said music of the shipwreck. I have noticed that with some of that music.
Also able to take in account is the similarities Hoenn has with other world destinations. The most likely inspiration is from Africa. Greece, as well as all of Europe, is desertless, while Africa's well known for its deserts. Also, many Hoenn Pokémon have similarities to African animals. I won't list them all here, but take a look for yourself sometime.
The point is, there is no official source claiming that Hoenn is based on Greece. Its unlikey, but not impossible.
