Any FileSystem could be a potential privacy risk. While one probably wouldn't want to encrypt a whole file system (although they might), it's likely that one would like to encrypt at least a few files. For example: one's banking files. The more concerned you are with your privacy the more files could fall into this category.
In windows NT variants you can mark files to be compressed on the fly to disk and uncompressed on the fly when accessed. In GE we could provide a mechanism that allowed files to be encrypted and decrypted on the fly. This would require some sort of authentication step at some point. Activating the screen saver might disable the authentication, for example. (depending on user prefs, of course)
This makes more sense on a MultiUser system than on a standalone box.
There are some things which can be done to brute force protect sensitive files on the fly on the BeOS system. Files can be encrypted, using a standard encryption algorithm such as the combination of the BlowFish Translator and the cryptic Tracker add-on. They are easy to use and effective, but the source file gets encrypted and decrypted in the same file, so be aware.
However, there is room for improvement in that when you launch an encrypted file it does not ask for a password resulting in applications being confused by the encrypted data. You specifically have to decrypt the file using the cryptic Tracker add-on. The source is available at the bebits page.