The "store annotations with documents" support introduced in Okular of KDE SC 4.9.0 requires >=app-text/poppler-0.20. Right now, it depends on >=app-text/poppler-0.12.3-r3.
Thanks for reporting. This is now fixed in CVS. + 03 Aug 2012; Johannes Huber <johu@gentoo.org> okular-4.9.0.ebuild: + Bump required dep on app-text/poppler by Elias Probst <mail@eliasprobst.eu> + wrt bug #429678.