HipChat encrypts the messages during transmission to the AWS server (as detailed here:http://help.hipchat.com/knowledgebase/articles/64445-is-hipchat-secure) but not on rest. As of now, there isn't any options to change the encryption type used for trasmission or storage.
Probably what would be beneficial to you (if the type of security used is a concern) is to opt in to the HipChat Server beta program where the local admins can store the message data anyway they choose on a local machine. You can sign up for the HipChat Server beta here: https://www.hipchat.com/server
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