Let $L=\langle \{R_i\}\cup\{f_j\}\rangle , i \in I, j\in J$ be a signature and consider the space of all L structures with countable universe $\mathbb{N}$. This space is mentioned in the paper here on the connection between topological dynamics (specifically extreme amenability of topological groups), structural ramsey theory and Fraisse theory.)
$$X_L = \Pi_i 2^{\mathbb{n}^n_i} \times \Pi_j \mathbb{n}^{\mathbb{n^m_j}}$$
It is mentioned in the paper that if $L$ is relational, then $X_L$ is compact (homeomorphic to $2^{\mathbb{N}}$.
The thing is, in general I am struggling to understand what the topology on this space is. It is just a countable product space of spaces with discrete topology. Is this space significant in any other contexts?
What you’ve written for $X_L$ isn’t quite right: it should be
$$X_L=\prod_{i\in I}2^{\Bbb N^{n_i}}\times\prod_{j\in J}\Bbb N^{\Bbb N^{m_j}}\;.$$
Saying that $L$ is relational is just saying that $J=\varnothing$, so that $X_L=\prod_{i\in I}2^{\Bbb N^{n_i}}$, which is the product of countably infinitely many discrete two-point spaces and therefore homeomorphic to $2^{\Bbb N}$. This is an extremely important space: it is homeomorphic to the (middle-thirds) Cantor set and in various guises crops up all over topology, real analysis, and set theory.
If $J\ne\varnothing$ and at least one $m_j>0$, $\prod_{j\in J}\Bbb N^{\Bbb N^{m_j}}$ is homeomorphic to $\Bbb N^{\Bbb N}$, the Cartesian product of countably infinitely many copies of $\Bbb N$ with the discrete topology, which in turn is homeomorphic to the space of irrational numbers with the topology that it inherits from the real line with its usual topology, a space that also crops up in a variety of places.
Topologically speaking, then, $X_L$ is homeomorphic to the Cantor set, the irrationals, or the Cartesian product of the two, and that product is actually homeomorphic to the irrationals, since $2^{\Bbb N}\times\Bbb N^{\Bbb N}=(2\times\Bbb N)^{\Bbb N}=\Bbb N^{\Bbb N}$, so it has a nice and very well understood topological structure.
Added: Andreas Blass reminds me that there are a couple of degenerate cases as well. When $L$ consists of nothing but a finite, non-empty set of constant symbols ($0$-ary function symbols), $X_L$ is homeomorphic to $\Bbb N$, a countably infinite discrete space, and when $L$ has no symbols at all, $X_L$ is just the one-point space.