A shipment is the process of transporting stuff. Cargo is what is being transported. So it's not like they're limited to water or land. Shipments can refer to water, land and air transports of cargo. And cargo obviously doesn't really mean anything but the goods that are being transported so there's not really a land/air/water thing involved. Shipment can also refer to the goods that are being shipped, but again there's no reference to the type of transportation.

A quick google search:
"The word cargo originates from the mid 17th century: from Spanish cargo, carga, from late Latin carricare, carcare 'to load,' from Latin carrus 'wheeled vehicle.' "
So it doesn't refer to a car at all, it refers to "loading" stuff. The "load"/"goods" or whatever you want to call it.