Let's put put the question in a bit more general context: Which type of metric spaces admit the property that nested closed balls can have empty intersection:
(1) Complete: Yes (as in the original post)
(2) Complete, normed: No (as in the answer)
(3) Compact: No: Take a converging subsequence of the midpoints of the balls
(4) Separable, complete, discrete: Yes, see below
(5) Convex closed subset of a separable Banach space: Yes, see below
(6) Wasserstein space of some Polish metric space: ???
...
Regarding (4): One can simplify the original example by only considering the sequence of midpoints from the original post. This should give something like
$(X = \mathbb N,d)$ with $d(m,n) := r(m\wedge n)$ where $\wedge$ denotes the Minimum and $r(n) := 1+ 1/n$. Then,
$$
B_{1+1/n}(n) = \{n,n+1,\ldots\}
$$
Clearly, these balls are nested and the intersection is empty, and the space is separable and discrete.
Regarding (5): we can isometrically embed the space $(X,d)$ into $\ell_\infty(\mathbb N)$ via a map $\phi : \mathbb N \to \ell_\infty(\mathbb N)$,
$$
n \mapsto r_n 1_{\cdot \geq n}.
$$
(Note that this is not the standard-embedding via the distance).
Let $Y \subset \ell_\infty(\mathbb N)$ be the closure of the convex hull of the image of $\phi$.
Now I claim that within $Y$, the balls $B_{r(n)}(\phi(n))$ are nested with empty intersection.
We first show $B_{r(n)}(\phi(n)) \supset B_{r(n+1)}(\phi(n+1))$ in $Y$.
For non-negative $f \in \ell_\infty(\mathbb N)$, we have
$$
f \in B_{r(n)}(\phi(n)) \Leftrightarrow f\leq r(n) + \phi(n)
$$
and the inclusion of balls follows as
$r(n) + \phi(n) \geq r(n+1) + \phi(n+1)$ and as
$Y$ only contains non-negative functions.
We now show empty intersection (clearly the balls intersect in $\ell_\infty(\mathbb N)$, but not in $Y$).
We can see that
$$
\mathbb R_+^{\mathbb N} \cap \bigcap_k B_{r(n)}(\phi(n)) = \{f \in \ell_\infty(\mathbb N) : 0 \leq f \leq 1\}.
$$
So we are left to show that no function in $Y$ is upper bounded by one.
Suppose such a function exists, call it $f_0$.
Clearly, $f_0\geq 0$ and $f_0$ is increasing and $ \|f_0\|_\infty = \lim_{k\to \infty} f_0(k) \geq 1$ (as $f_0 \in Y$). We will refine this to show that $\|f_0\|_\infty>1$.
Let $k \in \mathbb N$ be fixed with $f_0(k)>0$. For $\varepsilon >0$ let $f_\varepsilon$ in the convex hull of $\phi(\mathbb N)$ such that $\|f_0 - f_\varepsilon\|_\infty < \varepsilon$.
Choosing $\varepsilon$ small, we can ensure $f_\varepsilon(k) \geq 2(k+1) \varepsilon$.
We can write
$f_\varepsilon = \sum \alpha_i \phi(i)$ with $\sum \alpha_i = 1$ and $\alpha_i \geq 0$.
Hence,
$$
\sum_{i\leq k} \alpha_i r(i) = f_\varepsilon(k)
$$
But then,
\begin{align*}
\| f_\varepsilon \|_\infty = \sum_{i \in \mathbb N} \alpha_i r(i)
\geq \sum_{i\leq k} \alpha_i r(i) + \sum_{i \geq k} \alpha_i
&= 1 + \sum_{i \leq k}\alpha_i(r(i)-1) \geq 1 + \sum_{i \leq k} \alpha_i \frac{r(i)}{k+1} \\
&= 1 + \frac{f_\varepsilon(k)}{k+1} \\
&\geq 1 +2 \varepsilon
\end{align*}
But this is a contradiction to $\|f_0\|_\infty \leq 1$ and $\|f_\varepsilon - f_0\| \leq \varepsilon$.
In summary, we have found a convex closed subset of $\ell_\infty(\mathbb N)$ and a sequence of nested balls with empty intersection, showing (5).
Regarding (6), the 1-Wasserstein-space of (4) seems to not work (at least when inheriting the balls), as the balls are not nested anymore. But maybe more sophisticated examples are possible?