Conveyors are not scalable: they have terrible efficiency, maintenance, and capital costs. Conveyors are actually fantastically energy inefficient...worse than diesel trucks over anything longer than football field distances. Their rolling friction grows linearly with length. Furthermore, their number of moving parts grows linearly with length. And every roller added to the system has the potential to shut down the entire system...all it takes is a seized bearing. Routing efficiency is actually its strong point, which is why they are used in so many factory and logistics operations, but those are typically much smaller than manhattan.
That being said, there is definitely potential for underground logistics...but it is more likely to happen on rails or in tubes with vehicle propulsion instead of track propulsion.