Colorado State University in Fort Collins, Colorado has an extensive " Engines Lab" you could give them a call and see if you can talk to a prof there.
My guess...
The engineers intended for studs on the outside to help during assembly. Knowing that bolts into the water jacket have a tendency to be problematic they went with studs figuring that they would never be removed in the useful life of the engine.
Another thought. Perhaps they were used to secure the head during casting, or a blind hole would have required an additional part to the mold to create inside the head?
Or maybe the water passage inside thee is particularly tight and there was no room for more casting?