Of course, in classical logic, if you have $\forall x \forall y (P(x) \lor Q(y))$, then you can conclude $(\forall x, P(x)) \lor (\forall y, Q(y))$: if you didn't have that, then there would be $x$ such that $\lnot P(x)$ and $y$ such that $\lnot Q(y)$, and then that contradicts the assumption.
On the other hand, in intuitionistic logic, I don't think that necessarily holds. My counterexample is to work in the topos of sheaves on $\mathbb{R}$, let the domain of discourse be $\mathbb{N}^+$, and define $P(n) := (-\infty, \frac{1}{n})$ and $Q(n) := (-\frac{1}{n}, \infty)$. Then for any $m, n \in \mathbb{N}^+$, $P(m) \cup Q(n) = \mathbb{R}$, so the hypothesis should also be valid for any locally constant functions $m, n : U \to \mathbb{N}^+$, i.e. sections of the constant sheaf $\mathbb{N}^+$. On the other hand, $\bigcap_m P(m) = (-\infty, 0)$ and $\bigcap_n Q(n) = (0, \infty)$, and the union of those two is $\mathbb{R} \setminus \{ 0 \}$.
So, my question is to verify that this is a correct solution and I didn't miss anything silly. I would also be interested to see whether a counterexample could be constructed in terms of a Kripke frame, where no example immediately comes to mind for me.