One reason for not including negative integers is because we are solving an equation that is inverse of a polynomial. Specifically a monomial.
When we are taking $y^{n}=x$, if $n$ has to be positive integer, it must be because we are solving an equation that is the inverse of only a monomial function.In other words we are solving for the $n$th root by solving for the $y$ of the inverse of $x^{n}=y$
I believe the terminology of the roots of a function came from the definition of the $n$th root of monomials. The roots of the function or relation are the values where $f(x)=0$ or $f(y)=0$. Suppose $x=a$, where $a$ is real number, then the $n$th root means solving $y^{n}-a=0$. For more information look here.
In the case of the negative integer $n$ in $y^{n}=x$ we are solving for the $y$ of the inverse of a rational function (ex: $x=\frac{1}{y^2}$) but not the inverse of a monomial.
Now if there is no connection of $n$th roots to solving the inverse of a monomial, we could have included fractional values of $n$ (ex: $y^{1/2}=x$). However, then again, we are solving the inverse of a root function, not a monomial.
Edit: If we take $y^{n}=x$ and $n$ is an unreduced negative fraction and $x$ is negative number then there are certain problems with solving for $y$ ($y^{3}=-2$ is not $y^{6/2}=-2$ and $(-2)^{1/3}{\neq}(-2)^{2/6}$ since $\sqrt[3]{-2}{\neq}\sqrt[6]{(-2)^{2}}$) . On the other hand if n is a reduced fraction then there are no issues. Thus if $n$ is a reduced negative integer you can use the identity $x^{n}=\frac{1}{x^{-n}}$.