One of the features noted in the 1.0 release notes was improved support for TrueCrypt volumes. Some quick searching of the dropbox forums (
http://forums.dropbox.com/topic.php?id=14332) seems to indicate the since TrueCrypt uses a block cipher, dropbox should be able to only synchronize the changes (it's probably more bandwidth than the files alone, but certainly much better than having to sync the entire volume each time).