Many masked packages in x11-proto/ (they are consolidated in x11-base/xorg-proto) do not get removed with "emerge --depclean" since the package was not revbumped. Manual rebuild of package is required.
I am unsure whether further versions of the same package should be revbumped, too.
FWIW, it was my understanding that this would not happen for changes to DEPEND (but would happen for RDEPEND, hence version bumps when RDEPEND was changed). ulm summarizes how we're going to handle this, at least in the future (https://bugs.gentoo.org/656250#c7): <QA> This has been discussed before. Removing a dependency (and especially a build-time dependency) without a revbump is within the scope of our policy: https://devmanual.gentoo.org/general-concepts/ebuild-revisions/index.html The tradeoff is between some tiny packages like x11-proto/* remaining on users' systems, and the cost of rebuilding a large package like mesa. Eventually, these dependencies _will_ be dropped, e.g. on the next version bump of mesa. Also, it cannot cause any breakage on users' systems. </QA> I guess WONTFIX. Please just do a manual rebuild.