This one was very tricky, but just like with Mac's passcode, once you figure it out the clues piece it together quite cleverly.
So during your investigations you learn that during the daylight hours the rats are operating out of stores owned by mice that sell mouse essence, and all open and close at the exact same time.
Is there any store in-game that checks all those boxes? Yes. Aero's Junk. Go to the Western District and make a note of the exact time of day his shop opens and when it closes. In this case, 11:00 AM to 4:00 PM. So the combination lock in the sewer is 11000400.