The software that I like for encrypting drives is truecrypt. It's open source. And with a little knowledge, work, trial and error you could add certain functions of it into a usb loader. But no one here will take the time to do it. It would be a neat little feature to have, but if you're not pirating your games, and you're not selling pirated games, and you're not sharing pirated games then no one has any real reason to have their drive encrypted.
Although no one has fully ripped apart IOS59 (or at least I haven't seen it done yet), some people speculated that there could be some drive encryption feature built into that IOS, which may make it easier to do like you are wanting, but there is no legal way of obtaining IOS59 unless you were legally given the beta disc for Dragon Quest. So with that said, no one else will even bother to add in any features of IOS59 into any homebrew until it becomes available on NUS.
Sorry man, but you're out of luck here unless you want to start learning to code.