I found this in a googlegroups message:
Yes, pre-compilation reduces the time to load an application. This will
benefit you on your first request after a deploy, after you've been cycled
out or if more application instances are created to scale up with your load.
You will see up to 30% improved loading time on your first request.
Pre-compilation works by doing a bit of class loading work ahead of time in
the App Engine environment before the request comes in.
So it seems that precompilation is about optimizing load time, not runtime performance.