Is the gravitational force of Black Hole destroying Atoms? I have see answers to this question but they do not explain it well.
Atom is a relatively stable structure but containing 99.99999% "empty" space.
The empty space is not really empty, but that is not the question.
The question is, 
does the Atom gets so compressed to lose that "empty" space, and gets stripped of electrons by the gravity in Black Hole. If as Atoms get ripped apart will they add to the mass of Black Hole, resulting in more Gravity (growing Black Hole). So now one could say, the Atoms get converted into Gravitons ?
As a matter crosses the event horizon of a black hole it gets compressed down to Atoms and beyond.
We know that Atoms are electrically neutral (balanced). However if we strip it from an electron (by applying 30 keV) it would become positively charged (a Ion). What happens to that in Black Hole.
 A: Yes, the atom will be torn apart, and eventually in a Black Hole (BH) get ripped apart radially (to the BH) and get compressed into nothingness perpendicularly. 
Even before that happens the gravitational tidal force will rip off the electRons and have the nucleus break up and have most of it converted to neutrons, and then rip those off and get to the quarks, and eventually fall into the singularity. That's why we say that a BH forms when there is too much gravity, nothing can withstand the gravitational effects. Not electron pressure (which holds up white dwarf stars), not nuclear forces (neutron stars), and not strong forces (quark stars, or some parts of the cores of neutron stars). 
Yes, the equivalence principle says everything will be accelerated (i.e. pulled) the same way, but only until the force differential between two objects in the atom see different accelerations - that's the gravitational tidal effects, caused by very strong curvatures of the spacetime due to gravity. 
Now, that all according to classical GR. As they get closer to the singularity in the BH quantum gravity effect will increase, and we don't know what eventually happens because we still don't have a theory of quantum gravity. But the atomic components all get obliterated as explained above. Quantum gravity effects enter in after that, as the gravitational effects become even stronger, and smaller distance scales get affected. The characteristic distances at which this happens is on the order of the Planck length, about $10^{-33}$ cms, much less than the nuclear or quark scales.  
A: Due to the equivalence principle, an atom free falling into a blackhole is travelling inertially, and a comoving observer would not notice anything different about the atom.  Or at least that is how it works over small enough length and time scales. An extended object can feel tidal forces as it falls in.  
So until the tidal forces are appreciable over the length scale of an atom (really close to the singularity), the atom would not be appreciably changed. After that, yes the atom would 'collapse'.
Some stars that are not massive enough to form a blackhole at the end of their life will instead collapse into a neutron star. This is kind of like atomic matter collapsing into denser nucleus like matter.
