When we write an indefinite integral of a function $f(x)$, we write $\int f(x) dx$.
But we don't write the domain of $\int f(x) dx$.
For example, we don't write the domain of $\int \frac{\sin x}{1 + \sin x} dx$.
Why?
Definition of primitive functions from "Introduction to Analysis" by Kunihiko Kodaira:
Let $I$ be an interval.
Let $f(x)$ be a function defined on $I$.
If a function $F(x)$ which is defined on $I$ satisfies $F'(x) = f(x)$ on $I$, we call $F(x)$ a primitive function of $f(x)$.
Definition of indefinite integrals from "Introduction to Analysis" by Kunihiko Kodaira:
Let $f(x)$ be a function defined on an interval $I$.
We define an indefinite integral of $f(x)$ as a primitive function of $f(x)$.
We use $\int f(x) dx$ for an indefinite integral of $f(x)$.
It doesn't matter because derivarives and integrals are defined with limits. This takes care of any removable discontinuities (holes).
As to whole areas where the function is not defined (like the area left of the y axis for $f(x)=\sqrt{x}$), the derivative/integral of that function will be undefined in this area too, because you cannot possibly measure a slope or compute an area of a curve in an area where there is no curve.
So, all in all, the domain of the function doesn't matter. The driving intuition behind integrals and derivatives kind of requires you to assume those things.
(Note that if you extend everything to the complex plane, domains don't really matter except for indeterminate forms which limits take care of, and undefined points which, well, they are usually one of the complex infinities.)