The answer is yes. If $m=u^2+uv+v^2$ and $n=x^2+xy+y^2$, then
$$m=(u+\omega v)(u+\bar{\omega}v)\text{ and }n=(x+\omega y)(x+\bar{\omega}y)\,,$$
where $\omega:=\frac{1+\sqrt{-3}}{2}$ and $\bar{\omega}:=\frac{1-\sqrt{-3}}{2}$. Now,
$$\begin{align}(u+\omega v)(x+\omega y)&=ux+\omega (uy+vx)+\omega^2 vy=ux+\omega(uy+vx)+(\omega -1)vy
\\
&=(ux-vy)+\omega (uy+vx+vy)\,.\end{align}$$
since $\omega^2-\omega +1=0$. Thus,
$$mn=(f+\omega g)(f+\bar{\omega}g)=f^2+fg+g^2\,,$$
where $f:=ux-vy$ and $g:=uy+vx+vy$.
In fact, $S$ consists of all natural numbers of the form $$n:=3^\alpha \prod_{i=1}^r\,p_i^{\beta_i}\,\prod_{j=1}^s\,q_j^{2\gamma_j}\,.$$ where $\alpha,r,s,\beta_1,\beta_2,\ldots,\beta_r,\gamma_1,\gamma_2,\ldots,\gamma_s\in\mathbb{Z}_{\geq 0}$, $p_1<p_2<\ldots<p_r$ are prime natural numbers congruent to $1$ modulo $3$, and $q_1<q_2<\ldots<q_s$ are prime natural numbers congruent to $2$ modulo $3$. Note that, for such $n$, there are precisely $N_n$ pairs $(x,y)\in\mathbb{Z}\times \mathbb{Z}$ such that $n=x^2+xy+y^2$, where
$$N_n:=6\,\prod_{i=1}^r\,\left(\beta_i+1\right)\,.$$
For example, $N_3=6$ as $$(x,y)=\pm(1,1), \pm (2,-1), \pm(-1,2)$$ are all the integral solutions to $3=x^2+xy+y^2$ . Another example is $N_7=12$, since $$(x,y)=\pm(2,1),\pm(1,2),\pm(3,-1),\pm(-1,3),\pm(3,-2),\pm(-2,3)$$
are the integral solutions to $7=x^2+xy+y^2$. Also, there are $$\left\lceil\frac{N_n}{12}\right\rceil=\left\lceil\frac{1}{2}\prod_{i=1}^r\,\left(\beta_i+1\right)\right\rceil$$
pairs $(x,y)\in\mathbb{Z}_{\geq 0}\times\mathbb{Z}_{\geq 0}$ with $x\geq y$ such that $n=x^2+xy+y^2$.