Single file

All operating systems have fairly low limit on number of open file descriptors for a program and for all programs in total making this system resource one of the rarest. Furthermore operating over multiple files does not seem to bring in any substantial benefits for the database while it complicates its implementation significantly. The graph database typically needs to have access to the full graph at all times unlike say key-value stores or document databases. Splitting the data into multiple files would therefore be actually detrimental. Lastly overall storage taken by the multiple files would not actually change as the amount of data would be the same.

Conversely using just a single file (with a second temporary write ahead log file) makes everything simpler and easier. You can for example easily transfer the data to a different machine - it is just one file. The database can also operate on the file directly if memory mapping was turned off to save RAM at the cost of performance. The program would not need to juggle multiple files consuming valuable system resources.

The one file is the database and the data.