I just did a little test, and it seems to be sorted in the same way as if you go view > by type in the hypergraph. So, by type, then alphabetically. I only tested it with ~8 shaders, but are you sure that's not the case for you?
sry but how do you see them in the hypergraph? i selected all of them in the hypershade and clicked on "input and output connections", but they all appear in there and there are so many connections, other than that i can't seem to find a way to display the materials in the Hypergraph