There are numerous advantages to installing the NST on a hard disk.
You can adjust configuration files without losing your edits when you reboot.
You can adjust the default startup of the
NST. For example, you could have the NST come up with
snort enabled and checking the packets coming across
the eth1 interface and have Nessus
started and ready for use.
You can have permanent storage for SQL databases.
You can use the NST installation as a means to create your own custom network devices. Need to add some network attached storage, a print server, a kiosk like web browser, a departmental web server or SQL database? It doesn't take much to convert a NST hard disk install into any of these types of devices.
You can use the NST hard disk installation as a emergency boot partition should the operating system on your main partition fail to boot.