Yes and no.

This can happen even in languages like C when you do static linking.

The solution is to have the linker remove all code that is not being called. The consequence of it, it that you are restricted in doing reflection, for example.

Some Java native compilers allow you to provide a list of methods to leave alone, to avoid them being removed from the final executable.

Should be able to use ProGuard, a code obfusticator+trimmer for Java. http://proguard.sourceforge.net/

Although, from my experience doing Android with Scala, the process is slow.

What is large? Also, looking at software history, it will actually be cool in a few years to make binaries as large as possible. Files with random crap in them should be normal by then to show that you are the best value for money!