Will,
for serveletapi.jar we do include this as part of the JavaEE5 container that is automatically added to web projects. This container will not be deployed to web projects.
As far as other JAR is concerned, you could put it in a user library and add that to your project instead of adding the JAR directly. Then go to Window > Preferences > MyEclipse > Java Enterprise Project > Web Project and on the deployment tab, deselect “JARs from User Libraries”.
I realize this is not an optimal solution and I am prioritizing deployment filtering for the upcoming 8.6 release. Please let me know how it goes.