That is: is a subalgebra of a free Jónsson-Tarski algebra (aka Cantor algebra) again free?
I’ve almost convinced myself that it is, but (as with groups) a rigorous proof would be somewhat involved.
Perhaps there are general considerations implying this is true?
This is true, and it's pretty simple once you have a good normal form for elements of free Jónsson-Tarski algebras.
Let's first fix some notation. We will write $w(\cdot,\cdot)$ for the pairing operation on a Jónsson-Tarski algebra and $p_0,p_1$ for the two projections (so $p_0(w(x,y))=x$, $p_1(w(x,y))=y$, and $w(p_0(x),p_1(x))=x$). If $s=a_1\dots a_n$ is a finite string of $0$s and $1$s, we also write $p_s$ as an abbreviation for $p_{a_1}\circ p_{a_2}\circ\dots\circ p_{a_n}$.
Now fix a set $X$ and let $F$ be the free Jónsson-Tarski algebra on $X$. Let $T$ be the set of expressions of the form $p_s(x)$ for any string $s$ and $x\in X$. Define a reduced word on $X$ to be an expression obtained by repeatedly applying $w$ to elements of $T$, such that we never do an operation of the form $w(p_{0s}(x),p_{1s}(x))$.
Now we use this characterization to prove that certain subalgebras of $F$ are free. First, define a partial order $\leq$ on $T$ by saying $p_s(x)\leq p_t(y)$ iff $x=y$ and $t$ is a terminal segment of $s$. This makes $T$ a disjoint union of binary trees, one for each element of $X$. Say a subset $Y\subseteq T$ is independent if its elements are pairwise incomparable with respect to $\leq$ and there do not exist two elements of the form $p_{0s}(x)$ and $p_{1s}(x)$ in $Y$.
Finally, let $A\subseteq F$ be any subalgebra. Every element of $A$ can be obtained by repeatedly applying $w$ to certain elements of $T$, and those elements of $T$ must also be in $A$ since we can reverse $w$ using $p_0$ and $p_1$. Thus $A$ is generated by $A\cap T$. Let $Y$ be the set of maximal elements of $A\cap T$ with respect to $\leq$.
(In fact, it is easy to see that the constructions $Y\mapsto A$ and $A\mapsto Y$ above are inverse to each other, so that every subalgebra of $F$ is generated by a unique independent subset of $T$.)