When a photon falls into a black hole, the black hole increases in mass by m = E/c^2, where E was the energy of the photon. This is required by the conservation of energy and momentum. Energy can be thought of as the zeroth component of the momentum 4-vector, and each component of the 4-vector is conserved locally.
In general relativity, the curvature of spacetime is not caused by rest mass, but by the energy-momentum tensor.
http://en.wikipedia.org/wiki/Stress–energy_tensor
To answer the question of the box containing matter and antimatter:
5) The energy density of the box would not change, therefore the scale would still read as 20N
6) My question is, what is meant by "inertia"? This is a subjective question, because it doesn't refer to a measurable quantity, but to a phenomenon that is actually kinda complicated. This is usually called the conservation of energy and momentum. If you took the sum of energy and momentum of all the particles in the box before and after, then you would find it didn't change. In order to induce a change in the total energy/momentum of the box, there would have to be an opposite change in the energy/momentum of something else.
A better question that might be asked, suppose you had two boxes, one box full of normal matter, and one box made of half matter and half light. Say they are both placed on scales, and give the same number, 20N in this case. If both of them have the same total momentum not equal to zero in a particular direction (say the x-axis), then do they both travel at the same apparent velocity? Or does the half matter/light box have a higher velocity because it is "lighter?" Lol puns.
My intuitive answer is that they both move at the same velocity, but I haven't worked it out yet.
7) Mass is a loaded word, and not universally defined. If you're asking about the rest mass, then yes, the rest mass has changed. Photon have no rest mass, therefore the total rest mass of the box has decreased. However the photons do have energy and momentum. The energy and momentum of the photon could be said to have "gravitation mass" and that is conserved. The "gravitation mass" has not changed.