When you compile you do, yes. When you deploy, as long as you use the standard deployment (ie all classes in WEB-INF\classes and all jars in WEB-INF\lib) then no you don't as the container will do that for you.
An easy way arount the problem is to compile all the fairly static classes, that is classes that don't change much and put them into a jar file. Then your classpath will only need one jar file. Alternatively start looking at an IDE such as Eclipse which will do some of that hard work for you.