Is the substrate for the plants to grow in, rather than a pond liner? I'm not familiar with the design of natural swimming ponds. So the water is sucked through the substrate and into the bubbler and back to the pond?
On
his website he says that some subsoils maybe too rich in nutrients, but doesn't say anything about permeability. I'm inclined to agree with you that clay may not be the best to use. I suspect the plants would be OK, but the water would not be able to flow through it so easily. If you have a source of sand/gravel that seems sensible to use instead. Can you use the clay for landscaping instead?