Zeta functions, 3-manifolds and asymptotics in Nielsen theory

We prove that the Nielsen zeta function is a rational function or a radical of a rational function for orientation preserving homeomorphisms on closed orientable 3-dimensional manifolds which are special Haken or Seifert manifolds. In the case of pseudo-Anosov homeomorphism of surface we compute an asymptotic for the number of twisted conjugacy classes or for the number of Nielsen fixed point classes whose norm is at most x.