The Shafarevich conjecture/problem is about the finiteness of isomorphism classes of a family of varieties defined over a number field with good reduction outside a finite collection of places. For K3 surfaces, such a finiteness result was proved by Y. She. For hyper-Kähler varieties, which are higher-dimensional analogues of K3 surfaces, Y. André proved the Shafarevich conjecture for hyper-Kähler varieties of a given dimension and admitting a very ample polarization of bounded degree. In this paper, we provide a unification of both results by proving the (unpolarized) Shafarevich conjecture for hyper-Kähler varieties in a given deformation type. We also discuss the cohomological generalization of the Shafarevich conjecture by replacing the good reduction condition by the unramifiedness of the cohomology, where our results are subject to certain necessary assumption on the faithfulness of the action of the automorphism group on cohomology. In a similar fashion, generalizing a result of Orr and Skorobogatov on K3 surfaces, we prove the finiteness of geometric isomorphism classes of hyper-Kähler varieties of CM type in a given deformation type defined over a number field with bounded degree. A key to our approach to these results is a uniform Kuga-Satake map, inspired by She's work, and we study its arithmetic properties, which are of independent interest.