If your application shuts down the database in an orderly fashion, it can reduce the amount of work that the database has to do to start up again after an unexpected exit.
Derby features crash recovery that restores the state of committed transactions in the event that the database exits unexpectedly, for example during a power failure. The recovery processing happens the next time the database is started after the unexpected exit. Your application can reduce the amount of work that the database has to do to start up the next time by shutting it down in an orderly fashion. See "Shutting down Derby or an individual database" in the Derby Developer's Guide.
The Derby utilities all perform an orderly shutdown.