My personal opinion is that war graves should be free from penetration, one should experience them with ones eyes. There are plenty of other shipwrecks to penetrate.
I don't know. Assuming that your penetration is sufficiently skilled that you don't damage the wreck by diving on it (it had better be), actually being inside a "real" wreck can be one of the most sublime and moving experiences in diving. To see where they worked, ate, slept. I don't feel the same way about the San Diego as I do about an artificial reef.
Consider this, we may be the last generation to have historically significant shipwrecks to dive. No marine wreck lasts forever, and those of us who dive them can see the changes just over our few years of experience with the passage of winters and storms. With rare exceptions, shipwrecks don't happen any more. Collisions are thankfully becoming very uncommon, and clashes between huge navies with thousands of ships in combat doesn't seem to be the way that warfare is going.
Maybe you are making the distinction of a war grave, and those wrecks do get special protection by law. Being civilians, the 46 people who died on the Andrea Doria have to suffer their grave being a major draw for penetration over the years.