I'm using porthole-0.6.0-rc4.
When I select the Deprecated option, it shows me several packages where it says the installed version and recommended version are the same: phpmyadmin, libsigc++, and net-zope/zope. In each case, these are slotted builds and the ebuild for the oldest occupied slot has gone away.
e.g. net-zope/zope-2.10.6 and net-zope/zope-2.10.7 are installed in slots 2.10.6 and 1.10.7 respectively. There is no ebuild file for the 2.10.6 version.
I was curious what would happen, so I tried doing the unmerge using porthole - and it removed both versions rather than just the dud one.
Sorry for the long delay in responding. I was without internet for quite some time.
The deprecated view is very dumb indeed. So far all it does is list the installed packages/versions that did not find a matching ebuild/package for in any of the trees on the system. It is up to you to decide what you want to do with each and every one. The package details (installed, recommended) is the same basic code for all the views. So far there is no variances for the different views. I am open to someone helping come up with a good logic diagram or code to implement a smarter list and emerge policy to handle them.
But alass I am only one developer and my wife already compains about the "affair I am having with my computer" ;)