Well, I'm not sure if this would be of interest to you, but we can show the following: If a permutation $\pi$ of order 4 in $S_n$ for any $n \in \mathbb{N}$ that has a 4-cycle $(x_1,x_2,x_3,x_4)$ can be written $\pi=\sigma^2$, then $\pi$ must have at least two 4 cycles. This may be of interest because it will show that a permutation $\pi$ with exactly one 4-cycle cannot be a square even for instances where $\pi$ is an even number of transpositions [i.e., a 4-cycle and then a disjoint 2-cycle].
Claim 1: Suppose that $\pi=\sigma^2$ for some permutation $\sigma$. The size of the orbit of element $x_1$ must be exactly 8 under $H\doteq \langle \sigma \rangle$, and so the only element that fixes $x_1$ is $e$.
Indeed, the orbit of $x_1$ must have exactly 4 or 8 elements under $H$. If the orbit of $x_1$ has exactly 4 elements then there is a subgroup of $H$ of order 2 that fixes $x_1$.However, the only subgroup of $H$ of order 2 is $\{1,\sigma^2\}$ and $\sigma^2$ does not fix $x_1$. $\surd$
In light of Claim 1, the number of elements in the orbit $O_H(x_1)$ of $x_1$ under $H$ must be $|H|$, and for each $x_j \in O_H(x_1)$, the only element that fixes $x_j$ is $e$. So for each of the 8 elements $x_j \in O_H(x_1)$ and for any subgroup $H'$ of $H$, the number of elements in the orbit $O_{H'}(x_j)$ of $x_j$ under $H'$ must be exactly $|H'|$. So if $\pi=\sigma^2$ for some $\sigma$, then taking $H'=\langle \sigma^2 \rangle$ $=\langle \pi \rangle$; then $|H'|$ has exactly 4 elements, so for each of the 8 such elements $x_j$, the number of elements in the orbit $O_{H'}(x_j)$ of $x_j$ must have exactly 4 elements.
So it follows from this that each of the 8 elements $x_j \in O_H(x_1)$ is in a 4-cycle of $\pi$, so $\pi$ must have 2 4-cycles.
One can extend this line of reasoning to show that in fact $\pi$ must have precisely an even number of 4 cycles to be a square $\pi=\sigma^2$, where the elements in a 4-cycle of $\pi$ are precisely the elements in an 8-cycle of $\sigma$.
In fact, you could use this line of reasoning to show that a permutation $\pi$ in $S_n$ is a square iff for each $k \in \mathbb{N}$ there are an even number of $2k$-cycles.