It seems that atoms don't go away, they just get re-arranged.
Atoms consist of made by electrons, protons and neutrons.
The electrons orbit the nucleus which is made by the protons and neutrons. Bombs split an unstable nucleus to 2 others and 2 or 3 neutrons. These new neutrons split other nucleus and so on. So it seems that there is a set number of particles that cannot change. This process can give out enough energy to the point that it literally lights up the black hole, giving it it's name of white hole.