You definitely can but MongoDB provides convenience over storing and managing JSON files on you filesystem by your own efforts.
NoSQL or classic RDBMS, these tools give you ways to manage your data on the filesystem(or in the memory?). You can spend time to write a code that processes files in a folder or you can use the software that does it for you. You can write a code that relates two files in a folder or you can use a software that already can do it and you can just ask that software for the outcome.