Let $X$ be a compact Kahler manifold. Let $H^k = H^k_{prim} (X)$ be primitive cohomology of $X$ considered as an object in category of of polarized Hodge structures. We have a map \begin{equation*} h_k: Aut (X) \rightarrow Aut(H^k) \end{equation*} Question 1 Does $h_k$ have to be surjective for $k \neq 0, n$?
For boundary cases it obviously fails. You can not act non-trivially on $H^0$ via manifold automorphism. But $-1$ is a automorphism of Hodge structure.
Question 2 Do you know about some analogous statements which are theorems? Could you give source for them?
The homomorphism $h_k: Aut(X) \to Aut(H^k_{prim}(X,\mathbb C))$ is extremely interesting. Let me follow your notation and write $H^k$ for $H^k_{prim}(X,\mathbb C)$. Also, I will content myself to algebraic varieties in the discussion below.
Let me answer your first question. For a large class of varieties, the answer to your question is no. Indeed, the ``general" variety has no non-trivial automorphisms to start with. On the other hand, as you said, there is always the automorphism $-1$ of $H^k$. For example, the general cubic threefold $X$ has no non-trivial automorphisms (so $Aut(X) = \{id_X\}$), whereas $H^3$ is a $10$-dimensional polarized Hodge structure. Thus $h_3$ is not surjective in this case.
As you see, the surjectivity of $h_k$ fails quite often. It does hold in the case of complex tori as pointed out below in the comments.
To answer question 2 partially, let me point out that there is much work done on the kernel of $h_k$. These results (and the methods employed in their proof) might help you find the sort of statement you're looking for. Indeed, if $X$ is a curve of genus at least two, a principally polarized abelian variety, a hypersurface of degree at least three (and dimension at least two), a variety with very ample canonical bundle, or a hyperkahler variety with certain properties, then $h_k$ is injective; see Section 2.5 (especially Prop. 2.15) in http://arxiv.org/abs/1505.02249 .