Yes. In general, given any logic $\mathcal{L}$ with a notion of "length of formula" according to which every formula is finite and only finitely many formulas have a given length (not all logics have such length notions!) and any "ambient structure" $\mathfrak{A}$ containing the naturals, the Rayo function for $\mathcal{L}$ in $\mathfrak{A}$ makes sense. This is the function sending $n$ to the smallest number greater than every $k$ such that $k$ is definable in $\mathfrak{A}$ by an $\mathcal{L}$-formula of length $\le n$. See here for a summary of definability in the context of first-order logic; the basics remain unchanged when we replace first-order logic with some other logic, and an element is definable iff (by definition) the singleton containing it is definable.
Rayo's function as usually defined takes $\mathfrak{A}$ to be the whole set-theoretic universe $V$. This isn't properly speaking a structure, since it's too big, and this is what saves us from the apparent paradox. Similarly, in order to make sense of the Rayo function for $\mathcal{L}$ in $V$ we'll need to cheat and work in some "even larger" mathematical system. But ignoring this issue for the moment, the answer to your question is definitely yes: changing the logic can dramatically change the corresponding function.
Here's one easy observation: since in any "reasonable" structure $\mathfrak{A}$, first-order truth is second-order definable, the Rayo function for $\mathsf{SOL}$ (= second-order logic) in $\mathfrak{A}$ will eventually dominate the Rayo function for first-order logic in $\mathfrak{A}$. In fact more is true: the latter won't even be $O$-of-the-former.