Hinderburg-like at 100 ton itself can carry about 120 ton payload, ie. payload of 2 train cars.

And where does one dock this massive beast in a city with controlled airspace?

In a distribution center outside of the city the cargo is transferred onto local electric Amazon/UPS/etc. delivery trucks/vans.

So, the equivalent of a 100 car freight train would be a 50 Hindenburg zeppelin fleet?

It's actually fairly easy logistically imo

Design the Zeppelin for literal tons of ballast, trade out sandbags/dirtbags for product or waste on docking, andaybe add an aerodynamic shield if you don't care about speed as much

We already sacrifice significant speed for boats, but I grant they're several orders of magnitude better at balancing buoyancy with cargo given they flot in the water rather than atmosphere