I know it seems odd to say, but a fellow programmer at work deliberately used a couple of bad programming practices on purpose!  I'll explain.  First let me say that he's an intelligent guy and for the most part he writes intelligible code.  

He was asked to implement licensing on a web application project written in Java.  Since it's Java, if one really wanted to, one could probably hack open the jars and read the names of the classes and methods written inside.  His solution to this problem was to quite literally to awkwardly call variables and methods less-than-obvious names and plant them inside already congested classes rather than generating new classes.

His justification was that if a hacker wanted to switch out certain classes in order to bypass licensing checks (and therefore get a free copy of the product), he'd have a far more difficult time of it if it weren't obvious which methods perform these particular tasks.  Only after he had done it did I confront him about it, suggesting that we could perhaps buy some sort of obfuscator library to do it for us, while maintaining good programming practices.  He claims to not have had the time or resources to search for that kind of solution.

..Which leaves me at a dilemma.  Do I look for a obfuscator library in Java and fix his old code (which might be a little touchy about remodeling his code), or do I leave it as it, as much as that irks me to no end?

Security through obfuscation is never good security. There must be better ways of protecting your intellectual property. And that is what you and your colleague should bring up as a joint concern with your manager. If management then decide that they don't want to spend the time or money on improved security, then both of you will have to live with that decision (it's not your product, it's the company's product) and better not spend (waste?) any more time on the subject.