ksplash-ml installs to /usr/kde/3, even though my only kde dir is /usr/kde/cvs.
That is correct; under the current 'scheme' for multiple KDEs (to which 3.1_alpha1 and later (cvs) ebuilds confirm even when they are the only kde version installed) KDE apps go into /usr/kde/3 by default. Note though that recent kde-cvs tarballs have had a bug I only fixed a few hours ago where kdelibs doesn't register /usr/kde/3 in KDEDIRS and PATH, making apps installed there unrunnable. I'm going to upload a fixed version RSN (check for a kde-cvs-20020802-2 or 20020802-3 tarball in a few hours).