I can confirm Calibre Portable works on an external drive with TrueCrypt. I've been running it that way for years.
Once you have your drive encrypted with TrueCrypt, it mounts just like another drive, so you can install Calibre Portable there just fine.
The biggest drawback is how long it takes to initially encrypt the drive. Depending on the size of the drive and the speed of your computer, it might take several hours, although most of the process runs unattended (For full-drive encryption, I recommend letting it run overnight).
Make sure you go with TrueCrypt version 7.1a, NOT 7.2, which is insecure by design. (There are rumors as to why it's insecure, but suffice it to say that even the creators of TrueCrypt say you should not install 7.2)
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