You can always use encrypted loopback devices and test performance...
For FTP, it could be similar to SSH's scp and sftp, I don't know.
Making encrypted backups of these partitions has never been been easier... You could also encrypt /var/log
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You can however encrypt the files that you are serving and only authorized people have the key to decrypt it.
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There are many flaws with this setup:
1- You must trust all these users.
2- You must trust the computers they're connecting from.
3- If you change a password, you must notify these users.
4- Serving encrypted files over a plain-text protocol is dangerous because users may type the file's password at the login prompt. (Not to mention that their account passwords on your system may be sniffed as well, making your cryptography setup useless).
You must find the best option anyway, because it all depends on too much factors: the data being encrypted, etc...