paludis installs documentation into /usr/share/doc/${PN} but it should go to /usr/share/doc/${PF}. At the moment there are two doc dirs (/usr/share/doc/paludis, /usr/share/doc/paludis-0.42.2) as dodoc installs into /usr/share/doc/${PF}.
I'm sorry for not noticing this when I was working on 1.4.2. Since the ebuild is pretty fresh and the issue is pretty trivial, I have committed the fix retroactively to 1.4.2. People who installed that version already will get it on next rebuild/upgrade. + 20 Oct 2013; Michał Górny <mgorny@gentoo.org> paludis-1.4.2.ebuild: + Install API docs to proper htmldir, bug #296114.
No problem. Thanks for finally taking care of it!