Kudos for your work! Do you plan to integrate Amazon S3 the same way you did for hdfs?
First of all, you can file a feature request: https://github.com/Factual/drake/issues
Adding a new filesystem to Drake's source is very easy. You just create a filesystem object that implements a bunch of methods for: listing directory, removing file, renaming file and getting file's timestamps, and then put it along with the corresponding prefix in the filesystem map. That's pretty much it. Assuming there's client JAR for Amazon S3, written either in Clojure or in Java, it should be quite simple to do.
Artem.