The substitution is often driven by the domain of definition of the function under the integration symbol, this is because to be able to conserve the value of the integral, the change of variable must be bijective.
In our case for $\sqrt{1-x^2}$ to be well defined we must have $x\in[-1,1]$
So the choice of a function with a range in $[-1,1]$ is compulsory, there are several choices, for instance $\sin(x),\cos(x),\tanh(x)$.
Theoretically all would give the same end result, but some may lead to a nice result after substitution, for instance here we have the relations $\begin{cases}1-\tanh(x)^2=\frac 1{\cosh(x)^2}\\\cos(x)^2+\sin(x)^2=1\end{cases}$
In both cases $\sqrt{1-x^2}$ will transform to $\sqrt{(something)^2}$ and will simplify, but $\sin,\cos$ will result in rather nice $\int \cos^2,-\int \sin^2$ integrals while the last change will result in a less nice $\int \frac 1{\cosh^3}$.
Although notice that in the end, if you lead calculations to the end:
- the $\sin$ change will result in $\, \frac 12x\sqrt{1-x^2}+\frac 12\arcsin(x)$
- the $\tanh$ change will result in $\, \frac 12x\sqrt{1-x^2}+\arctan(\frac{x+1}{\sqrt{1-x^2}})$
It may appear different, but they just differ by a constant value $\frac{\pi}4$, so the choice of the variable substitution doesn't change the result, just take the one that leads to the simpler calculation.
Here are two other examples
$\displaystyle \int x\sqrt{\frac{x-1}{x+1}}\mathop{dx}\, $ and $\, \displaystyle \int \frac{x^4}{\sqrt{x^2-9}}\mathop{dx}$
Notice that for the first one, we need $x-1\ge 0\implies x\ge 1$ and for the second one $x\ge 3$ or $\frac x3\ge 1$.
Both suggest a function whose range is $[1,+\infty)$, and we know that $\cosh$ is such a function, also since it is a trig function the relation $\cosh^2-\sinh^2=1$ also leads to nice simplifications. And indeed, such a substitution allows to solve both integrals effectively.