Another at InsideScience includes information about other sites such as Chichen Itza, where the echo of a hand clap in front of the stepped monument comes back as a chirp. Having been there and experienced the phenomenon first hand, I can say it's a very striking effect that seems to be more than happenstance.
These articles reminded me of visiting "Agamemnon's tomb" in Greece, and having had some time alone in it between tour groups. The video at the link gives a taste of the reverberation inside it, and I'd find it hard to believe the people that built it didn't notice the acoustics and put them to use somehow.
The InsideScience article also mentions something I'd seen before, that cave paintings are often in the most acoustically interesting parts of the caves.
I always wonder how anyone can say with any certainty what the people of those long ago times were up to, but since all the new neuroscience points to just how important sound and music are to the human brain, that they were aware of that in their own way and somehow put it to use wouldn't surprise me at all.