Welcome to MathOverflow. A good reference for such a question is
Goldberg, H.; Kampowsky, W.; Tröltzsch, F., On Nemytskij operators in $L^p$-spaces of abstract functions, Math. Nachr. 155, 127-140 (1992). ZBL0760.47031.
(In fact, the paper is even about Nemytskii operators between vector valued [Bochner] Lebesgue spaces, but of course one recovers the results for real-valued spaces.)
Since the Nemytskii operator acts on the function $u$ only, you would consider $L^r(\Omega)$ such that $W^{1,p}(\Omega) \hookrightarrow L^r(\Omega)$ (Sobolev embedding, e.g. $\frac1r = \frac1p - \frac1N$ if $p < N$) and then use Theorem 9 in the above paper to find out when $F$ is twice continuously differentiable as an operator $L^r(\Omega) \to L^q(\Omega)$.
The conditions would be that ...
- $2 \leq 2q < r < \infty$ or $r = q = \infty$,
- $f$ is twice continuously differentiable with respect to the
$\mathbb{R}$ component, say, $y$,
- the partial derivatives $f_y$
and $f_{yy}$ satisfy Carathéodory measurability conditions as
functions $\Omega \times \mathbb{R} \to \mathbb{R}$, and finally
- the Nemytskii operator $G$ induced by $f_{yy}$, $$[G(u)](x) :=
f_{yy}(x,u(x))$$ is continuous as a mapping $L^r(\Omega) \to L^s(\Omega)$, where $s = \frac{rq}{r-2q}$ if $r < \infty$ and $s = \infty$ if $r=\infty$.
For the last condition, there are necessary and sufficient conditions in Section 2 in the paper, depending on finiteness of $q$ (and $s$). For instance, if $q < \infty$, then it is sufficient that $$|f_{yy}(x,y)| \leq \gamma(x) + \beta |y|^{\frac{r}{s}} \quad ((x,y) \in \Omega \times \mathbb{R})$$ for some $\gamma \in L^s(\Omega)$ and $\beta \geq 0$. (See also Remark 7 in the paper.)