Does Backup Exec back up the data from Microsoft SQL .ndf files, as well as the .mdf and .ldf files?
Yes, Backup Exec does automatically protect the data residing within the .ndf files along with the .mdf and .ldf files.
It might be noticed that the database backups are smaller in size than expected based on the added values of the .mdf, .ldf, and .ndf files added together, but this is normal.
To verify that the size of the backups are correct, perform a database dump from within SQL and then compare the dump size to the Backup Exec backup size. They should have approximately the same amount of data.
An alternative way to confirm that the data is being protected correctly is to simply perform a restore of the database(s) or SQL server(s) in question. Restores can be redirected to another system so as not to disturb a production environment.
Note: Symantec recommends that test restores are periodically performed, just to familiarize yourself with recovery procedures and iron out any issues that may arise during the process.