It occurred to me that Martijn van Buul wrote in gmane.os.netbsd.general:
> *apperently* an rmdir of a non-empty directory in a union-mounted fs
> *succeeds*, turning a harmless "rmdir /usr/pkg/bin" into the equivalent of a
> "rm -rf /usr/pkg/bin".

Small update: This only happens in a chrooted environment.