Thule does not sell replacement cargo carrier tops or bottoms. The components are riveted together, which Thule considers a permanent attachment. These can only be attached safely using machinery at Thule's production facility.
The carrier shells also cannot be shipped via UPS/FedEx and, like the boxes themselves, must be shipped via freight. The freight charge for this mode of transport would far exceed the cost of the part. The shells themselves get their rigidity from being attached together, so a single part of the shell would likely be damaged in shipping.
You can attempt to repair a crack or break in a ski/cargo box using an epoxy or ABS patch kit. These products can be found at a big box hardware or marine supply store. An ABS patch kit, similar to what you would get for a bike tire, is designed to adhere to certain types of plastic and fiberglass. An epoxy kit, once applied and cured should seal up the crack and prevent further spreading.
Thule does not warranty any repairs as we have not tested them and cannot ensure their safety or strength under highway conditions.