Containers were smaller, and were not stacked as high. Cardboard cartons were not yet common, or were small and light enough to be stacked by one person. Other goods were in burlap or canvas bags that could be hefted over a worker's shoulder, or in kegs/drums/barrels that two workers could roll up plank ramps and then wrestle upright. Wooden crates could, as you suggest, be lifted with a sling or hook and then swung into place. Grains and minerals were typically moved using shovels, belts, and screw transports.

The modern single-level high-cube warehouse is entirely an invention of the truck-and-forklift age, and the need to minimize labor costs. Earlier warehouses had lower ceilings, but multiple floors in any area where land costs were relevant.