As it was pointed in the comments, if $G$ and $H$ are counterexamples and $K$ is an arbitrary finite group, then $G \times K$ and $H \times K$ also form a counterexample. And if $(G_0, H_0)$ and $(G_1, H_1)$ are both counterexample pairs, such that $G_0 \times G_1$ and $H_0 \times H_1$ are non-isomorphic, then $(G_0 \times G_1, H_0 \times H_1)$ is also a counterexample. So there are definitely infinitely many counterexamples (and your conjecture is equivalent to “there are finitely many counterexamples”, as for any $n \in \mathbb{N}$ there are only finitely many groups of order $n$).
Now let’s prove something stronger.
Let’s call counterexample pair $(G, H)$ non-primitive, if it is of the form ($G_0 \times G_1$, $H_0 \times H_1$), where $(G_0, H_0)$ is a counterexample, and primitive otherwise. It turned out, that, despite those restrictions, there are still infinitely many primitive counterexamples.
Suppose $Q_{8n} = \langle x, y | x^{4n} = y^4 = e, x^{2n} = y^2, y^{-1}xy = x^{-1} \rangle$ and $D_{4n} = \langle a \rangle_{4n} \rtimes \langle b \rangle_2$. These groups are counterexamples for any $n \in \mathbb{N}$. And they are also all primitive because there is no nontrivial direct decomposition of $Q_{8n}$.
One can see, that $Var(Q_{8n}) = Var(D_{4n})$ as $Q_{8n}$ is isomorphic to a subgroup of $\frac{(\langle a \rangle_{4n} \rtimes \langle b \rangle_2) \times (\langle c \rangle_{4n} \rtimes \langle d \rangle_2)}{\langle a^{2n}c^{2n} \rangle}$ (a homomorphic image of $D_{4n} \times D_{4n}$), generated by $a$ and $c^nb$, and $D_{4n}$ is isomorphic to a subgroup of $$\langle x, y, z, t| x^{4n} = y^4 = z^{4n} = t^4 = e, x^{2n} = y^2 = z^{2n} = t^2, y^{-1}xy = x^{-1}, t^{-1}zt = z^{-1}, [z, x] = [z, y] = [t, x] = [t, y] = e \rangle$$ (a homomorphic image of $Q_{8n} \times Q_{8n}$) generated by $x$ and $z^ny$.
One can also see, that both $D_{4n}$ and $Q_{8n}$ have the unique minimal nontrivial normal subgroup. In case of $Q_{8n}$ it is $\langle y^2 \rangle$ and in case of $D_{4n}$ it is $\langle a^2 \rangle$. And it is also quite obvious, that $\langle y^2 \rangle \cong \langle a^2 \rangle \cong C_2$ and that $\frac{Q_{8n}}{\langle y^2 \rangle} \cong \frac{D_{4n}}{\langle a^2 \rangle} \cong C_2 \times C_{2n}$.
Now suppose $A$ is some set of group words. If they are all identities in $D_{4n}$, then they are also identities in $Q_{8n}$, as $Var(D_{4n}) = Var(Q_{8n})$, which results in $|V_A(D_{4n})| = |V_A(Q_{8n})| = 1$. Now suppose, that some of them are not identities. Then $|V_A(D_{4_n})| > 1$ and $|V_A(Q_{8_n})| > 1$, which results in $\langle y^2 \rangle \leq V_A(Q_{8n})$ and $\langle a^2 \rangle \leq V_A(D_{4n})$. Now, as a homomorphic image of a verbal subgroup of a group is always the verbal subgroup of the homomorphic image of the group in respect to the same set of group words, we can conclude, that $$|V_A(D_{4n})| = |\langle a^2 \rangle||V_A(\frac{D_{4n}}{\langle a^2 \rangle})| = 2|V_A(C_2 \times C_{2n})| = |\langle y^2 \rangle||V_A(\frac{Q_{8n}}{\langle y^2 \rangle})| = |V_A(D_{8n})|$$