Unfortunately I have to report that the bug is still there, as it has more or less mysteriously returned on my OS X system.
After being able to work with Eclipse/JBoss tools for some time without any problems, the missing WEB-INF/lib directory after a fresh start of Eclipse suddenly returned. I did make one change to my installation recently, and that is install MercurialEclipse. In an existing workspace, I deleted the SVN projects I normally worked on, and cloned those again from our central Mercurial repository (my company has migrated from SVN to Mercurial). A little later, although not immediately I got the missing WEB-INF/lib again.
The problem seems to be 100% reproducible. Every time I start Eclipse I have the problem. The old trick of closing and opening a project, followed by a clean (redeploy) brings WEB-INF/lib back. The problem doesn't surface again as long as I don't restart Eclipse.