Alessio I don't think this is a bug, this behaviour seems consistent.
Consider that you have old projects that could be compiled and linked without any problem, why they should be modified to include new folders with libraries that they evidently don't need?
Moreover for some projects you may have used libraries, or includes, with conflicting names, this will not allow you to recompile your old projects unless major change.
On the other hand if you reorganize your libraries, moving them around in different directories, the small overhead to fix project paths should be considered a natural conseguence.
For same reason it have to be considered correct that if you create new libraries, that can potentially be used in all future projects, the system adds their directories in freshly created projects.
One more consideration is about the creation of new folders and libraries, for the same issues explained before you have to create global folders only for very standard libraries (as the C standard lib are) to avoid problems where you use different versions or tailored libs in your projects.