I have found a temporary way to better do this.
I still use matlabs built in jsonencode function, and output a JSON file, but I do it in small stages/chunks. For example, I have a devision factor, which determines how many chunks I do. This then splits the data structure into row indices. I then encode the json within those row indices, and write that chunk of data to the file. I then go onto the next chunk and so forth until all data is written.
If someone is in need of the code then let me know and I can provide it. It does not take any less time than a single jsonencode call would be, however greatly reduces load and memory consumption on the computer, and can be made to be 32-bit compliant (each chunk cant be larger than ~1gb)
