A friend suggested a solution, which I will sketch below. It relies on some rank conditions that are hard to interpret, but it is better than nothing.
(1) If either $f$ or $g$ is strictly convex, then (as I have already assumed a solution exists) there exists a unique solution $x(y)$.
(2) If $f$ and $g$ are continuously differentiable and one imposes assumptions so that the constraint binds, then this solution and its associated Lagrange multiplier (which exists by convexity) are $N+1$ unknowns solving a system of $N+1$ equations (first order condition plus constraint). If $f$ and $g$ are twice continuously differentiable and some rank conditions hold, one can apply the implicit function theorem to argue that $x(y)$ is continuously differentiable.
(3) Theorem 3 of Milgrom & Segal (2002) is an envelope theorem implying that---under some conditions implied by those assumed in (2)---$V(y)$ is differentiable and $V_y(y) = -f_x(x(y))$. (Here it helps to rewrite the problem as suggested by Ilya's comment on Math Stack Exchange.) Since $f(x)$ and $x(y)$ are both continuously differentiable, so is $V_y(y)$. So $V(y)$ is twice continuously differentiable.