Those libraries are "private" to Kid3, and versioning them results in a wrong feeling of those libraries having a public API. Furthermore, versioning is done without respect to rules of the environment the Kid3 is built for (e.g., on OpenBSD shared libraries have ".major.minor" suffix, unlike ".major.minor.patch + symlinks" on Linux).
Thus I propose simply dropping VERSION assignment for kid3-core and kid3-gui libraries. Less code is always better, isn't it? :)