Zeno of Citium is known to the world as a GREEK philosopher, not a Cypriot one (of Pheonician origin).
Aphrodite is known to the world as a GREEK goddess, not a Cypriot one (again, as it happens, of Pheonician origin).
Zeno - Because back when he was born, Cyprus was regarded as a Greek island, and Zeno was born in Cyprus. Secondly, Zeno was taught Greek philosophy in Athens. So it seems that this is where the assumption lies. He was culturally, if not ethnically, Greek.
Aphrodite - The Cypriot religion was the Greek religion. So she was a Cypriot and Greek goddess. It was the same thing.
See, you seem to assume that the Cypriots and the rest of the Greeks are and always were separate, this is why your conclusions are slightly wide of the mark.