Since there is no surviving treatise on the "theory" of given names, so to speak, the best we can do as scholars is draw conclusions from the examples available. The main tool for this purpose is the Lexicon of Greek Personal Names, which collects hundreds of thousands of individual ancient Greek names, mostly gleaned from inscriptions. I've discussed the basic principles in this older thread.

The decoding of Linear B in the early 1950s allowed us to establish that some Greek names are very old, including some names of Olympian gods and Homeric heroes. Hittite letters written in Luwian in the Late Bronze Age suggest the existence of a king Alaksandu at Troy, which may be a rendering of the Greek name Alexandros (Alexander). But the record from this early period is very thin, and since writing disappears in Greece after the end of the Bronze Age, we do not know how many names have origins that far back or which names were actually used until writing is reintroduced some 400 years later.

Similarly, it is very hard to say anything about the evolution of Greek names, since the record is extremely uneven. Until the Hellenistic period, Athens is practically the only city with a strong epigraphic tradition. For most communities in the Greek world we have only a smattering of names until the Roman period, if at all. How are we to say which names were old and which were innovations? The only names of which we can be certain that they were new were theophoric names referring to newly introduced gods (such as Isidoros, "gift of Isis," or Christophoros, "bearer of Christ"). These cannot predate the introduction of the related cult in the place where they are attested.

As to names that seem strange, there is again little we can say for certain, because no ancient Greek ever explains their origins. It certainly doesn't seem like anyone thought a name like Xenophon was an odd choice; there are multiple Xenophons of note (including a Xenophon son of Euripides, mentioned by Thucydides). As I wrote in the other post, some names referred to physical features (not always flattering, like the nickname Platon, which should probably be read as "Fivehead"), but many others to rivers or notable places, traits and habits, and most frequently, to the gods. The choice was free and there does not appear to have been any social resistance to any name except those of underworld gods.

In short, the answer to your question how much we know about the origin and evolution of ancient Greek given names is that we know basically nothing. Origins are obscured by the complete lack of evidence for several crucial centuries of Greek cultural development. Meanwhile, there are not enough preserved value judgments about names, and there is not enough observable change in the repertoire, to draw any conclusions about trends in naming.