Bad news
The second derivatives need not converge a.e. or even in measure. Indeed, let $g_n(x)$ be the $n$th binary digit of $x$. Then the antiderivatives $G_n(x)=\int_0^x g_n(t)\,dt$ uniformly converge to $x/2$, and second antiderivatives $f_n(x)=\int_0^x G_n(t)\,dt$ uniformly converge to $f(x)=x^2/4$. However, $|g_n-f''|=1/2$ a.e.
(In this example, $f_n$ is not twice differentiable, but one can fix this by smoothing $g_n$ a little; this doesn't really matter for integral estimates.)
Good news
Distributional convergence is inherited by derivatives of all orders. This means that for any test function $\phi\in C_c^\infty((0,1))$ we have
$$
\int_0^1 f_n'' \phi\,dx \to \int_0^1 f''\phi\,dx
\tag{1}$$
This is not particularly surprising: it's just a restatement of the obvious
$$
\int_0^1 f_n \phi''\,dx \to \int_0^1 f \phi''\,dx
$$
via integration by parts.
But we can do better: (1) holds for all continuous functions $\phi$ with compact support in $(0,1)$. In other words: interpreting $f_n''$ as a measure (which it is), we have weak convergence of measures on compact subsets of $(0,1)$. Here is why:
- The measures are bounded on each interval $[a,b]$ with $0<a<b<1$, since $f_n'(a)$ and $f_n'(b)$ are uniformly bounded (controlled by convexity & uniform convergence).
- By Banach-Alaoglu, every subsequence $f_{n_k}''$ has a weakly convergent subsequence $f_{n_{k_j}}''$.
- Since weak convergence of measures implies distributional convergence, the limit of $f_{n_{k_j}}''$ is $f''$.
- General topology fact: if every subsequence has a subsubsequence converging to the same limit, then the whole sequence converges there.