I was thinking about the set $\left\{(x,y)\,\middle|\,x^2+y^2 = \frac{1}{n^2}, n \in \Bbb{N}, x\in \Bbb{Q}\text{ or }y \in \Bbb{Q}\right\}$
Certainly, this set is non-empty as I can find a pair $\left(\frac{1}{n^2},0\right)$ or like $\left(\frac{1}{2n^2},\frac{1}{2n^2}\right)$ or in a more genral sense the points of the form $\left(\frac{a}{n^2},\frac{b}{n^2}\right)$ where $a+b = 1, a,b \in \Bbb{Q}$, so hence I think it's a countable set?
But there may be some irrational coordinates involved which can make the set uncountable?. Can we rule out this possibility?
Your set is a countable union of countable sets:$$\bigcup_{n\in\mathbb N}\left\{(x,y)\in\mathbb{R}^2\,\middle|\,x^2+y^2=\frac1{n^2}\wedge x\in\mathbb{Q}\right\}\cup\left\{(x,y)\in\mathbb{R}^2\,\middle|\,x^2+y^2=\frac1{n^2}\wedge y\in\mathbb{Q}\right\}.$$Therefore, it is countable. Each of these sets is countable because, for instance, for each $x\in\mathbb{Q}$, the equality $x^2+y^2=\frac1{n^2}$ can only occut to finitely many $y$'s.