Could you split libraries when they are no longer backward compatible (so they don't appear in `qpkg --dups`). Big ones I know of are db and freetype (I know freetype-1.x and freetype-2.x are not compatible at all). By this I mean: freetype-1.4.2 and freetype2-2.0.4 or whatever. I mean, PHP3 and PHP4 are still mostly compatible, so they don't need it. When libraries do that jump, they are typically not compatible w/ each other. This will become more prominent as libraries in Linux get rewritten due to poor original implementation. (I know SDL will do it and GTK+ & GLIB are in the process of it.)
This is solved by binary compatibility slots, now in testing.