Pure coincidence. The names of both cities predate major contact between Egypt and mainland Greece and are totally unrelated. Boeotian Thebes is among the oldest cities in Greece--Homer seems to think of it as the oldest, since when he says that something is older than Thebes or happened before Thebes was built that means it's unimaginably distant. Egyptian Thebes is called "Waset" in Egyptian, but the nearby template complex at Karnak is called "ta-opet" (it's been some time since I took Egyptian--and I was never very good at it--so for the life of me I don't remember what "opet" means, although "ta" is simply a demonstrative standing as a de facto article). In New Egyptian the name often morphed into "ta-pet," which is how it's written in Demotic. This is the name often used to refer to the temple complex during the period of Greek contact with Egypt starting at least at the beginning of the Archaic Period. By association the term was applied to the city as a whole and rendered as "Thebai" in Greek, probably due to linguistic assimilation with the name of the Greek city.

It's also worth noting that Egyptian Thebes had a number of other names in both Greek and Egyptian. As the seat of the Cult of Amun the city was also called the City of Amun, or "nwt-imn," a name that appears frequently in religious and official texts. The Greeks directly translated the name as "Diospolis," or City of Zeus, due to the assimilation in Greek thought of Amun as a foreign aspect of Zeus