I have to find the best possible $k\in\mathbb{N}$ such that for all sufficiently big $n\in\mathbb{N}$ less than $1$% of all permutations $[n]$ have at least $k$ fixed points.
I don't really understand the question to be honest. I already showed that $D(n)=n! \sum_{k=0}^n \frac{(-1)^k}{k!}$ and $\sum_{k=0}^\infty \frac{(-1)^k}{k!}=\frac{1}{e}$
Let $S_n$ be a uniform random permutation in $\mathfrak{S}_n$. Call $F_n$ the number of fixed points of $S_n$. The distribution of $F_n$ can be computed explicitely by enumerating the permutations in $\mathfrak{S}_n$ having exactly $k$ fixed point: for every integer $k \in [0,n]$, $$\mathbb{P}[F_n=k] = \frac{{n \choose k}D(n-k)}{n!} = \frac{D(n-k)}{k!(n-k)!}.$$ Hence, for every $k \in \mathbb{N}$, $\mathbb{P}[F_n=k] \to e^{-1}\frac{1}{k!}$ as $n \to +\infty$: in other words, the distribution of $F_n$ converges to Poisson law with parameter 1.
Hence for every $k \in \mathbb{N}^*$,
$$P[F_n \le k-1] \to \sum_{\ell=0}^{k-1} e^{-1}\frac{1}{\ell!}.$$ If you find the integer $k \ge 2$ such that $$\sum_{\ell=0}^{k-2} e^{-1}\frac{1}{\ell!} < 0,99 < \sum_{\ell=0}^{k-1} e^{-1}\frac{1}{\ell!},$$ you are done.