I have an example showing how other tricky problems can be embedded in this problem that may be more satisfactory because the ring itself is more tractable. It may also be less satisfactory because there is, I think, still an algorithm to solve this problem. The GCD in question will be the ring of formal sums of knots.
The equivalence classes of knots form a commutative monoid $M$ under the knot sum, so we can define a monoidal ring $\Bbb{Z}[M]$, which is made up of elements that look like $3A + 4B - 2C$ where $A, B, C$ are knots, and you multiply two knots by taking the knot sum $\#$, and this multiplication is extended to every element of $\Bbb{Z}[M]$ linearly, like you would expect, i.e.
$$(aA + bB) \cdot (cC + dD) = acA\#C + adA\#D + bcB\#C + bdB\#D$$
Because of Schubert's Theorem, $M$ is freely generated by the prime knots, so $\Bbb{Z}[M]$ is isomorphic to the polynomial ring over $\Bbb{Z}$ with countably many generators- which is a UFD, hence also a GCD. But the problem of determining if an element is square includes the problem of determining whether a knot $A$ can be expressed in the form $B \# B$.