Ignorabimus
Several of the Hilbert problems have been resolved (or arguably resolved) in ways that would have been profoundly surprising, and even disturbing, to Hilbert himself. Following Frege and Russell, Hilbert sought to define mathematics logically using the method of formal systems, i.e., finitistic proofs from an agreed-upon set of axioms. One of the main goals of Hilbert's program was a finitistic proof of the consistency of the axioms of arithmetic: that is his second problem.
However, Gödel's second incompleteness theorem gives a precise sense in which such a finitistic proof of the consistency of arithmetic is provably impossible. Hilbert lived for 12 years after Gödel's theorem, but he does not seem to have written any formal response to Gödel's work. But doubtless the significance of Gödel's work to mathematics as a whole (and not just to formal logic) was amply and dramatically illustrated by its applicability to one of Hilbert's problems.
Hilbert's tenth problem does not ask whether there exists an algorithm for deciding the solvability of Diophantine equations, but rather asks for the construction of such an algorithm: "to devise a process according to which it can be determined in a finite number of operations whether the equation is solvable in rational integers." That this problem was solved by showing that there cannot be any such algorithm would presumably have been very surprising to him.
In discussing his opinion that every mathematical problem should have a solution, Hilbert allows for the possibility that the solution could be a proof that the original problem is impossible. Famously, he stated that the point is to know one way or the other what the solution is, and he believed that we always can know this, that in mathematics there is not any "ignorabimus" (statement that the truth can never be known). It seems unclear whether he would have regarded the solution of the tenth problem as an instance of ignorabimus: what we are proving not to exist is not the integer solution, but (in a certain sense) our own ability to discern whether a solution exists.
On the other hand, the status of the first and second problems is even more complicated: there is not any clear mathematical consensus as to whether the results of Gödel (in the case of the second problem), or Gödel and Cohen (in the case of the first problem) give definitive negative solutions or not, since these solutions apply to a certain formalization of the problems, a formalization which is quite reasonable but is not necessarily the only possible one.
Read more about this topic: Hilbert's Problems