I agree, with the addition that if the data is being assembled to send between companies, then go with the format that is most easily understood, most clearly documented and which is least likely to have internal data inconsistencies. All of those criteria favor the nested version.

One additional advantage to the nested format is the data is physically closely associated. This reduces time going back and forth across the file/disk to find data, which can be the biggest delay when the file is too big to fit into memory.