If encryption is enabled (Preferences > Notes > Security), neither the data nor the metadata of any note will ever be written to disk in clear text, even temporarily. Even the number of notes and their relative lengths are fully opaque. By ensuring that no unencrypted data will ever touch the disk, the problem of secure file deletion can be avoided entirely.
Notational Velocity uses the OpenSSL implementation of AES-256 in cipher-block chaining mode. However if AES-128 proves more secure, the DB preferences format would make using an alternative key size straightforward.
The write-ahead log file, which stores changes not yet written to the database, is also encrypted using keys ultimately derived from the password.
Because it’s inevitable that the contents of Notational Velocity’s memory will be swapped to disk at some point, users should enable Secure Virtual Memory in the Security preferences panel in Mac OS X.
Additionally, to prevent unauthorized access while Notational Velocity is left running, users should also enable Require password to wake this computer from sleep or screen saver from the same panel, and set the screen saver to activate after some period of time.