Suppose we have two maven projects.
One is CDI/Seam/JSF (any kind of project that requires KB builder/nature).
The other is a plain java project.
The first one includes the second one as a dependency.
When our maven intergration plugins enables CDI/Seam/JSF they also should enable KB support for all the dependencies (direct or indirect ones).

You can enable KB via org.jboss.tools.jst.web.kb.WebKbPlugin.enableKB(IProject project, IProgressMonitor monitor)

So CDI/Seam/JSF (KB included) should be enabled for the first project.
And KB should be enabled for the second one.