Emerald-0.9.5 has dependency on emerald-themes, portage demands unmasking emerald-0.8.8 which doesn't work with current compiz, the whole reason for emerald. I copied the Funtoo 1.2 emerald-themes to local repository, then portage agreed to install emerald and emerald-themes. However, after emerald completed successfully, the emerald-themes ebuild could not d/l the source. Yet the source hasn't changed, is still available. The problem lies in the ebuild, it has:

SRC_URI="http://cgit.compiz.org/fusion/decorators/${PV}/snapshot/${P}.tar.bz2"

While it should be:

SRC_URI="http://cgit.compiz.org/fusion/decorators/${PN}/snapshot/${P}.tar.bz2"

Summing up:
1. emerald-themes IS required in tree
2. the ebuild needs repair
3. Additionally, the Manifest is wrong, needs rebuilding
After making these changes both emerald and emerald-themes are installed here.