MacJournal stores all of the data that is entered in a window into a single file. By default, MacJournal creates a file named "MacJournal Data.mjdoc" and places it in a folder inside your user folder in the Finder. However, more documents can be made using the File menu inside MacJournal, which will open a new window, and this can be saved to a new location in the Finder with any name (but still end with "mjdoc"). No data is stored inside the MacJournal application itself and uninstalling or upgrading MacJournal does not remove any user data.
The MacJournal data file appears in the Finder as a single file, however it is a file that contains many other files inside of it. By holding the Control key and clicking on any MacJournal data file in the Finder, you can see the files inside the data file by choosing "Show Package Contents". Inside is a folder named "Content", in which contains one file for each entry in that document. MacJournal stores these files in standard formats like RTF and plain text. These files can be opened in other applications should MacJournal not be available at the moment for some reason. Files for entries in encrypted journals are combined to a single file and then encrypted and appear in that Content folder with an "mjenc" file extension.
Next to the Content folder is a file called "index.mjml.gz". This file contains all of the metadata and hierarchy of the entries and journals. This includes the topics and tags for entries, and what entries are in what journals. When MacJournal saves out entry text into the Content folder, it also tries to include this metadata in the file, but that is only used as backup data; the real metadata are all stored in the index file.
Some display settings like window sizes and sidebar visibility are stored in a file with your username that ends in "mjuser". The last selected entry is also saved in this file. This file can be deleted without deleting any entry text or metadata. If you open MacJournal with the Shift, Control, Option, and Command keys held down, this file is ignored and default settings are used. This can be useful if you are having any issue starting up MacJournal due to what was selected previously.
There can also be some other files inside the data file, including files for the content search index and files used to remember data between syncing with iOS devices.