On your export, set the page size to 1 as this will ensure that the records with the same document ID are grouped into a single "rows record," and then each page will have only one row record. From there, on your import, enable skip aggregation so that one file is made per page of data. This assumes each file only contains one document ID because if it includes multiple document IDs, then this will make a JSON file for each document ID, as opposed to one JSON file per CSV.
If you truly need one JSON file per CSV file, as opposed to one JSON file per document ID, then you’ll need to make an export that is a folder saved search that returns a list of all CSV files in the folder you want to export. From there, set your page size to 1. Then make a lookup to get the actual contents of the file and parse it as CSV. Response map the returned data to your main record. Then you get to your import step and again set skip aggregation to true. You should probably use mapper 2.0 as well to get it into the format you want. You can see this method here: Netsuite File Cabinet File .
