ncbi-tools++: fix prefix libdir, muparser/hdf5 use flags

This patch fixes three things:

 * prefix `--libdir`: libraries are installed in `${PN}`, but `runpath` is set to be `$(get_libdir)/ncbi_cxx`. This results in libraries not found when trying to run the built executables (as reported in #274)
 * `USE=muparser`: `./configure` can fail because `--with-muparser=...` is given but no matter what the `USE` flag is set to, and `dev-cpp/muParser` is not necessarily installed
 * `USE=hdf5`: `./configure` fails to find `libhdf5_cpp`, which is only built for `sci-libs/hdf5[cxx]`