They had metal working and also knew how to work clay. Plus finding water leaks isn’t difficult to know what specific points need attention, then you just add material until it stops leaking. The pipes might have been large enough to work from the inside if the flow was diverted.

They also wouldn’t need a perfect seal, just a good enough seal that the majority of the water makes it to the other side.

I’d bet that there were teams of people whose full-time job was to maintain each of the siphons rather than the more modern approach of “build it and then bury it under asphalt because it will probably be fine for years” plumbing takes today.