OS X does not slow down, but Java applications may be a step slower than carbon or cocoa applications because they are running in the Java Virtual Machine. When Carbon and Cocoa applications are compiled they result in a binary code that is directly executable by the PowerPC processor in your Mac. When Java applications are compiled, they are compiled to a "virtual machine language" that is the same regardless of the hardware platform the application is running on. Then when you run the application the Java Virtual Machine software in OS X must translate the JVM instructions into the PowerPC (or pentium or whatever) machine language to be executed.
Java may not be quite as fast as native code, but it is far more portable across hardware and OS platforms. A principal reason Java is a four letter curse word in Redmond, Washington.