Lowering the Prelude does make it look even more rad, IMO.
However, correct me if I'm wrong, but it also lowers your roll center...meaning the car wants to make a bigger arc when it "rolls" while cornering. This makes it handle worse.
The benefits of lowering it a bit might outweigh this, in the form of a lower center of gravity, but the bigger handling difference you're noticing from lowering the car is probably just from the stiffer springs!
That being said, my car IS slightly lower than stock, but really only because that's where it sits with Neuspeeds and Konis...either slightly higher or slightly lower.