1: There aren't that many access areas for the waste to enter from.
2: There are a ton of sealed off doors, some of which have a firey light leaking out the bottom.
3: There are tons of crates and wagon wheels stored down there.
4: Massive amphitheaters and hallways which would be completely unnecessary.
5: Light can be seen in the massive cracks in the boss fight room ceiling, meaning at least part of it is unlocked.
6: None of the houses are shown to have bathrooms, and in fact the rooms in Anor Londo have chamber pots.
7: Lots of bars blocking doorways. Stopping Debris is one thing, but that's just ridiculous.
8: The boss fight room has turrets and walkways. What would they be in that massive room FOR?
Quite frankly, it all adds up to point at something other then a sewer, but I won't deny it is designed to channel water. Is it a storm drain system to funnel water away from the cities? Was it a prison for the undead/criminals that are sealed off behind the doors? Some kind of third choice or combination?