I think the Shivans are, in the long run, meant to symbolize the great anthropocentric uncertainty of mankind.
Are we the right path for life in the cosmos? Or are we some kind of dead end, a bunch of overly specialized, under-adapted planetdwellers with flawed cognition and a backwards social structure? When we go out there, are we going to find ourselves shuddering in the face of something so truly superior and unknowable that, no matter how hard we strive, we cannot avoid extinction?
The Shivans are an embodiment of the possibility that the cosmos are an inimicably hostile place, and that we are only apes brandishing sticks and posturing at the uncaring darkness.