I would say that this is probably not the best practice because of the version: how do I know which version of the application you have deployed? If you deploy the .war file, the build process can take care of updating the build number (from the original control or separately, no matter how each has a different number, that's OK).
If you use continuous integration (and this is definitely a good idea), then your build process should pop up an “artifact” (war file) every time you make changes to the source code. also possibly tagging version control with build number.
So, when you deploy your web application, you know exactly which version works and what source code makes up this version.
Making small incremental changes by updating individual .class files, I would say, is probably not a good idea for anything other than testing a local developer.
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