Mavericks does encrypt backups. From Apple:
The best way to keep your backups secure is to encrypt your backup
disk. Encryption is available for Time Capsule, disks attached to
another Mac on your network, and disks partitioned with the GPT
partition scheme and attached directly to your Mac.
If you want to change from unencrypted to encypted backups, you must
remove your backup disk and then set it up again.
So, if you have an existing backup, you'll need to remove them from the backup disk you'd like to be encrypted. You should be able to see the encryption status of your backup on a per-volume basis in the
Time Machine pref pane.