In ebuild-mode.el: (defcustom ebuild-mode-portdir "/usr/portage" "Location of the ebuild repository." :type 'string :group 'ebuild) Should be updated to /var/db/repos/gentoo.
In git: https://gitweb.gentoo.org/proj/ebuild-mode.git/commit/?id=b951aa72de5720119e16cc419e72230eaa33d9ff
Fixed in ebuild-mode-1.45. The default is now /var/db/repos/gentoo, with a fallback to /usr/portage if the former directory doesn't exist.