That did not happen for me.

WHM 11.11.0 cPanel 11.15.0-R17665
CENTOS Enterprise 4.5 x86_64 on standard - WHM X v3.1.0

I compiled in Tomcat via EA3 and my existing java sites came up working just fine and it did NOT add any additioanl public_html/WEB-INFO/ folders or files to sites that did not have servlets installed recently.

Mike