I have a theory to what they are.
In microbiology bacteria can be free roaming, like the smaller zurks in the game, but bacteria often will form biofilm, a collective of many individual bacteria to form a mass, a film that usually clings to something, and grows. The most interesting thing about biofilms is quorum sensing, in which a biofilm, which can have a population of varying bacteria, mold, fungi, protozoa and viruses etc. together, actually sets up a self regulating system.
Quorum Sensing allows the mass to control genes. Some are turned on or off, to do various different functions for the collective biofilm, such as defense, growth, virulence, bioluminescence, chemical secretion and many more other potential functions. And on top of it, biofilms are much more harder to kill than individual free swimming bacteria, they often have much higher resistance to the typical physical, chemical and radiation factors that could damage or kill them. Dental plaque is an example of biofilm, the fresh stuff is easy to brush away, the older stuff is more mineralized and becomes hard and difficult to remove.
So....The eyes in the sewers could very well be a "biofilm". The makeup of the biofilm could be non roaming zurks, but also human genetics and organic material. The dead can provide growth resources but also genetics to various different resistances and growth hormones and regulators. If this biofilm was able to engulf live humans, human consciousness or intelligence, could possibly also be added to this large organism, due to the functioning neurological pathways in a live human compared to a dead one, the functioning bio pathway could have been rapidly integrated. Think how fungi can hijack an ant's living body to do weird behavior and climb to a point where it then dies and the fungi sporulates.
The biofilm could perhaps even enhance whatever body systems and genetics from humans with any companion and computer operating systems as well. So we have the rapidly evolving, growing and virulent zurks, engulfing other organisms, and organic matter like many bacteria do, breaking them down and taking what materials they need to perform typical growth, but also randomly conserving parts that may become beneficial to them and it replicates, grows, and mutates forever more as time goes on.
The eyes look like that of an animal, with eye lids and round pupil, it follows and have rather many expressions, and gives off a look of curiosity, and observing nature. This is a feature of animals, especially humans, but they also have a defensive response to be able to call in the free roaming zurks. So you have a higher intelligence behavior, paired with the rapid hive mind flooding to a stimuli, like microphages onto on a foreign body.
The sewer eyes has to be a massive biofilm of zurk, human and whatever other micro or macro organisms that were dumped into the sewers.
