Depending on how the car was cared for and stored the roof box's condition can vary a lot. If the car was left outside and the outer door seals are bad, the box fills up with water and rots. If it is only surface rust (no actual holes) you can clean it up and paint it with POR 15 or equivalent. No way to spray or brush it so you use a rag and a wire or a stick and just slobber it all around. Before deciding what to do, an inspection is a good idea. It may not be as bad as you think or it could be a whole lot worse. It is worth trying to save it if you can, replacing it is a big job.