In my attempt I will prove the following inequality:
$$
\boxed{u_n \geqslant \arctan(u_0)}
$$
which implies, that the limit of that sequence is not $0$ and gives us some nice lower bound for that sequence.
In my approach I will use some results derived by @Cactus and @Math-fun in their solutions.
Let's at first notice that:
$$
u_n = 2^n \arctan\left(\frac{1}{2}\arctan\left(\dots\left(\frac{1}{2}\arctan\left(\frac{u_0}{2}\right)\right)\right)\right)
$$
where we compose $\arctan$ function $n$ times. This motivates us to denote sequence $\{x_n\}$, where $x_0 = u_0$ and $x_n = \arctan(\frac{x_{n-1}}{2})$. This gives us relation $u_n = 2^nx_n$. Values of $x_n$ are for sure positive.
We have the identity $\arctan(x) \leqslant x$ that holds for all positive real values of $x$. This allows us to write:
$$u_0 \geqslant \arctan(u_0)$$
Now let's notice that:
$$
x_n = \arctan\left(\frac{x_{n-1}}{2}\right) \leqslant \frac{x_{n-1}}{2}
$$
If we apply that identity $n-1$ times, we will get:
$$
x_n \leqslant \frac{x_1}{2^{n-1}} \implies x_n^3 \leqslant \frac{x_1^3}{2^{3n - 3}} \implies 2^{3n-3}x_n^3 \leqslant x_1^3 \qquad (1)
$$
which we will use later.
To prove the result I will use induction with the following (stronger) claim:
$$
u_n = \boxed{2^nx_n \geqslant \arctan(u_0) + \frac{x_1^3}{9\cdot2^{2n-3}}} > \arctan(u_0)
$$
Base case for $n = 1$.
We have:
$$
2x_1 \geqslant \arctan(u_0) + \frac{2\cdot x_1^3}{9} \iff 2\arctan\left(\frac{x_0}{2}\right) \geqslant \arctan(x_0) + \frac{2}{9}\cdot\arctan\left(\frac{x_0}{2}\right)^3
$$
Replcaing $\frac{x_0}{2}$ with $t$ tells us, it is sufficient to show, that:
$$
f(t) = 2\arctan(t) - \arctan(2t) - \frac{2}{9}\cdot\arctan(t)^3 \geqslant 0 \qquad \forall t > 0
$$
We have:
$$
\lim_{t\to \,+\infty} f(t) = \pi - \frac{\pi}{2} - \frac{2}{9} \cdot \frac{\pi^3}{8} = \frac{18\pi - \pi^3}{36} > 0 \qquad \text{(because $\pi^2 < 18$)}
$$
This implies, that: $ \exists t_0\forall t > t_0: f(t) > 0 $. So after some point $f(t)$ is positive so we can pick some $t_1 > t_0$ and then $f(t_1) > 0$. In addition we have $f(0) = 0$.We know that, $f(t)$ is continuous, so it has some minimum in the interval $[0, t_1]$. With what was said, the minimum is either $0$ or some value $f(t)$, where $t \in (0, t_1)$. But $f(t)$ is also differentiable, so if it has a minimum in $(0, t_1)$, then in that point we have $f'(t) = 0$.
Now I will show that: $f'(t) = 0 \implies f(t) \geqslant 0$.
We have:
$$
f'(t) = \frac{2}{3\cdot(1 + t^2)(1 + 4t^2)}(9t^2 - \arctan(t)^2(1 + 4t^2))
$$
Now:
$$
f'(t) = 0 \iff 9t^2 - \arctan(t)^2(1 + 4t^2) = 0 \iff \arctan(t) = \frac{3t}{\sqrt{4t^2 + 1}}
$$
Moreover we can observe that, if this equation has a solution, then $t > 1$. By way of contraditction, take $t \leqslant 1$, then $\arctan(t) \leqslant \frac{\pi}{4} < 1$. In addition we have $\arctan(t) \leqslant t$. So now:
$$
9t^2 - \arctan(t)^2(1 + 4t^2) \geqslant 9t^2 - t^2 - 4t^2 = 4t^2 > 0
$$
and this is the contradition.
Now let's take $T > 1$ such that $\arctan(T) = \frac{3T}{\sqrt{4T^2 + 1}}$ (if such $T$ does not exist, then we immedietely have $f(t) \geqslant 0$ $\forall t > 0$)$^{(*)}$. Additionally I will use the fact $\arctan(t) \leqslant \frac{\pi}{2}$.
$$
f(T) \geqslant 2\arctan(T) - \frac{\pi}{2} - \frac{2}{9}\arctan(T)^3 = h(T)
$$
I can use equality $\arctan(T) = \frac{3T}{\sqrt{4T^2 + 1}}$ to obtain:
$$
h(T) = \frac{6T}{\sqrt{4T^2 + 1}} - \frac{\pi}{2} - \frac{6T^3}{(4T^2 + 1)\sqrt{4T^2 + 1}}
$$
$$
h(T) \geqslant 0 \iff 6T - \frac{6T^3}{(4T^2 + 1)} \geqslant \frac{\pi}{2}\sqrt{4T^2 + 1}
$$
LHS and RHS of the last inequality are both positive for $T > 0$, so we can square them. Then we can multiply both sides by $(4T^2 + 1)^2$ and after rearranging terms we will obtain:
$$
(324 - 16\pi^2)T^6 + (216 - 12\pi^2)T^4 + (36 - 3\pi^2)T^2 - \frac{\pi^2}{4} \geqslant 0
$$
Let's substitute $z = T^2 \quad(T > 1 \implies z > 1)$.
$$
g(z) = (324 - 16\pi^2)z^3 + (216 - 12\pi^2)z^2 + (36 - 3\pi^2)z - \frac{\pi^2}{4} \geqslant 0
$$
Now:
$$
g'(z) = 3(324 - 16\pi^2)z^2 + 2(216 - 12\pi^2)z + (36 - 3\pi^2)
$$
From inequality $\pi^2 < 10$ we can deduce that all coefficients of that quadratic function are positive, and thus it is positive for $z > 0$, so $g(z)$ is increasing.
For $z = 1$ we have:
$$
g(1) = 576 - \frac{125\pi^2}{4} > 0
$$
And since $g(z)$ is increasing for $z > 0$, we have $g(z) > g(1) > 0$ for $z > 1$.
Therefore we have:
$$
f(T) \geqslant h(T) > 0
$$
And thus we have $f(t) \geqslant 0 \quad \forall t > 0$.
Inductive step.
I will use inequality $\arctan(x) \geqslant x - \frac{x^3}{3}$ here.
We have:
$$
\begin{align}
2^{n+1}x_{n+1} = 2^{n+1}\arctan\left(\frac{x_n}{2}\right) \geqslant 2^{n+1} \left(\frac{x_n}{2} - \frac{x_n^3}{3 \cdot 2^3}\right) = \\ = 2^nx_n - 2^{n-2}\frac{x_n^3}{3} \geqslant \arctan(u_0) + \frac{x_1^3}{9\cdot2^{2n-3}} - 2^{n-2}\frac{x_n^3}{3}
\end{align}
$$
It suffices to show now, that:
$$
\frac{x_1^3}{9\cdot2^{2n-3}} - 2^{n-2}\frac{x_n^3}{3} \geqslant \frac{x_1^3}{9\cdot2^{2n-1}}
$$
$$
\frac{x_1^3}{9\cdot2^{2n-3}} - \frac{x_1^3}{9\cdot2^{2n-1}} \geqslant 2^{n-2}\frac{x_n^3}{3}
$$
$$
\frac{x_1^3}{3\cdot2^{2n-1}}\geqslant 2^{n-2}\frac{x_n^3}{3}
$$
$$
x_1^3\geqslant 2^{3n-3}x_n^3
$$
but this is exactly $(1)$. So the proof is finished.
$^{(*)}$ as noticed by @user472228 such $T$ in fact exists and $ T\approx 13.91$