Yeah, there's clearly some more connection between cytonics and delvers than we've seen. It can't just be that cytonics draws delvers here and delvers are just some random creatures of the deep. Spensa takes on Delver emotions just by using her powers - there's something there.I agree that whatever the delvers are, they weren't around during DE timeframe.
I don't think the delvers are former humans (or other species) though. Spensa had to basically teach this Delver that the little specks were also people and not just buzzing dust. If the delvers were formerly people, they would know this already.
My guess as to what brought the Delvers forth - the portals to mine acclivity stone, portals to Nowhere. They weren't around during DE time, because they seem to be a combination of Cytonics and technology, the kind of thing that wasn't around until humanity expanded on cytonics. We see the same strange markings near the portals, and in the Delver maze. I think these portals somehow brought the Nowhere closer to our plane. (Reminds me of the Cognitive Realm and perpendicularities, from the Cosmere...) This would be why there's so many delvers, so close, every time cytonics is used - acclivity mining (and exiling) via nowhere portals has been going on, full bore, for a very long time.
I don't have a good guess for how the delvers are connected to cytonics yet. My best guess is that the delvers are the source of cytonic power - and cytonic individuals are those that can draw on the nearest delver, or on a particular Delver. (Like people in the Cosmere that get Investiture from a Shard.) This connects them to that delver.
I don't know how AI fits into this. Maybe cytonic AIs can draw on more delver power than unaided people, and thus both grow very powerful themselves AND anger the delvers very, very quickly?