In an expression where more than one random variables are involved, the symbol $E$ alone does not clarify with respect to which random variable is the expected value "taken". For example
$$E[h(X,Y)] =\text{?} \int_{-\infty}^{\infty} h(x,y) f_X(x)\,dx$$
or
$$E[h(X,Y)] = \text{?} \int_{-\infty}^\infty h(x,y) f_Y(y)\,dy$$
Neither. When many random variables are involved, and there is no subscript in the $E$ symbol, the expected value is taken with respect to their joint distribution:
$$E[h(X,Y)] = \int_{-\infty}^\infty \int_{-\infty}^\infty h(x,y) f_{XY}(x,y) \, dx \, dy$$
When a subscript is present... in some cases it tells us on which variable we should condition. So
$$E_X[h(X,Y)] = E[h(X,Y)\mid X] = \int_{-\infty}^\infty h(x,y) f_{h(X,Y)\mid X}(h(x,y)\mid x)\,dy $$
Here, we "integrate out" the $Y$ variable, and we are left with a function of $X$.
...But in other cases, it tells us which marginal density to use for the "averaging"
$$E_X[h(X,Y)] = \int_{-\infty}^\infty h(x,y) f_{X}(x) \, dx $$
Here, we "average over" the $X$ variable, and we are left with a function of $Y$.
Rather confusing I would say, but who said that scientific notation is totally free of ambiguity or multiple use? You should look how each author defines the use of such symbols.