inkscape-0.46-r1 doesn't have pdf in its IUSE since bug 213706 was resolved. However, the configuration still does "$(use_enable pdf poppler-cairo)" so at the moment, poppler support won't be enabled even if the pdf USE flag is given. There is even a QA notice to that effect. As this bug affects the runtime behaviour of already installed packages, the fix should bump the revision.
Fixed in media-gfx/inkscape-0.46-r2. Thanks for the report.