The Schwarzschild solution in GR only has a singularity at the origin 𝑟=0:
Inside the horizon, the Schwarzschild r coordinate is timelike, not spacelike. Therefore it's not correct to imagine that as $r\rightarrow0$, one is getting close to a point in space that is the center of symmetry. As $r\rightarrow0$, one is getting close to the end of time, and this is the way it's depicted on a Penrose diagram.
As other answers have pointed out, there is no underlying spacetime that extends all the way to the singularity. Topologically, the singularity is a hole cut out of spacetime.
Usually Dirac-delta type singularities in 3D can be detected by doing a surface integral around them either very close or at infinity and observing that the result is non-zero.
Gauss's theorem fails in curved spacetime for nonscalar quantities, because adding fluxes requires comparing vectors at different places, but that can only be done by parallel transport, which is path-dependent. The mass-energy density is not a scalar, it's a component of a rank-2 tensor, so Gauss's theorem doesn't give you a way to find the mass-energy inside a surface. We can observe the distant gravitational field of a black hole and use it to find a mass. Conceptually, you can think of this mass as the mass-energy of the gravitational field in and around the black hole. But the equivalence principle guarantees that we can never localize the mass-energy of the gravitational field, since the gravitational field at a given point can always be zero if you are an inertial (free-falling) observer.
A Schwarzschild black hole is not an astrophysical black hole. In spacetimes that describe a black hole that formed by gravitational collapse, we can try to trace what happens to the infalling matter. There is a lot of variety in the things that can happen, and it's not really well established, for example, whether the singularity starts out being a naked singularity and then later on becomes a spacelike singularity more like a Schwarzschild singularity. We also don't really know for sure whether there is initially a strong curvature singularity, in which the volume of a cloud of infalling test particles goes to zero. A Schwarzschild black hole doesn't have a strong curvature singularity, it has a spaghettifying singularity.
Although the details of the process of realistic astrophysical gravitational collapse are an open question, it's probably roughly correct conceptually to say the following. As a black hole collapses, the mass-energy of the infalling matter gets converted to a mass-energy of the black hole's gravitational field. Because of the technicalities of how the Einstein field equations are expressed, this gravitational field energy is inherently delocalized, and does not appear as a term in the stress-energy.