This is an interesting thought, thank you.
Hydrus was originally going to do something like this–sending encrypted chunks across a p2p net to provide cloud storage, but the program has ultimately focused on more on local file management. Getting files from other people is actually fairly easy, while tagging things in a reasonable amount of time is difficult, so my programming time has focused on the latter.
And as >>1370 says, encryption is no panacea. I can encrypt files or the database, but if someone who doesn't like you has access to your hard drive via some clever spying method, you are basically screwed no matter what you do. I would still advise everyone to run generic disk encryption like truecrypt, but I think I will leave hydrus's individual files fast and unencrypted for now.
Encrypting network traffic however is something I do want to move towards. I will be experimenting with IPFS this week, and I have a long term plan to encrypt all hydrus client-server traffic.