Henceforth let $U=(0,1)$.
IN SUMMARY: You need to be careful about the spaces which you are talking about, and what norms they are equipped with. Letting $X$ and $Y$ be normed spaces each with two different norms $\Vert\cdot\Vert _{X},\Vert\cdot \Vert'_X$ and $\Vert\cdot\Vert _{Y},\Vert\cdot \Vert'_Y$ , an arbitrary mapping $T:X\to Y$ may be closed when considered as an operator from $(X,\Vert \cdot \Vert_X)\to (Y,\Vert \cdot \Vert_Y) $, but may not be closed when considered as an operator from $(X,\Vert \cdot \Vert'_X)\to (Y,\Vert \cdot \Vert'_Y)$, when these two pairs of norms are not equivalent.
Understanding $A$ as an operator from $(H^2(U),\Vert \cdot \Vert_{H^2(U)})\to (L^2(U),\Vert \cdot\Vert_{L^2(U)})$, $A$ is quite obviously closed. The reasoning is as follows: Clearly, $A$ is linear. Therefore, via the closed graph theorem, $A$ being continuous implies $A$ is closed. So it suffices to show $A$ is continuous, or equivalently, $A$ is bounded.
In other words we would like to show that $\exists C>0$ such that
$$\Vert Au\Vert_{L^2(U)}\leq C\Vert u \Vert_{H^2(U)}$$
But $A=-D^2$, in other words
$$\left\Vert -D^2 u\right\Vert_{L^2(U)}\leq C\left(\Vert u\Vert^2_{L^2 (U)}+\left\Vert D^1u \right\Vert_{L^2(U)}^2+\left\Vert D^2 u \right\Vert^2_{L^2(U)} \right)^{1/2}$$
Which clearly holds - just take $C=1$.
(As in the other question, we now take a symmetric interval $U=(-1/2,1/2)$
As shown in the answer to your other question, this is not the case when we consider $A$ as an operator from $(\text{domain},\Vert \cdot\Vert_{L^2(U)})\to (L^2(U),\Vert \cdot \Vert_{L^2(U)})$.
Here, $$\text{domain}=\{u:U\to \mathbb R~\text{such that}~u\in C^2(U)\cap H^2(U),~u(-1/2)=u(1/2),~Du(-1/2)=Du(1/2)\}$$
Again, $A$ is linear, so in order for $A=-D^2$ to be closed it must be bounded. Therefore, there would need to exist $C>0$ such that
$$\left\Vert D^2 u \right\Vert_{L^2(U)}\leq C\Vert u\Vert_{L^2(U)}$$
$\forall u\in \text{domain}$. But, for instance consider the sequence $(u_k)_{k\in \mathbb N_0}\in\text{domain}$
$$u_k(x):=x(1/2+x)(1/2-x)\exp(-k^2x^2)$$
You can check $\Vert u_k \Vert_{L^2(U)}\to 0$ as $k\to\infty$, however $\left\Vert D^2 u_k \right\Vert_{L^2(U)}\to\infty $ as $k\to\infty$ (which takes some work, but it is doable) .
Thus no such constant $C$ can exist.