I assume that at a certain power level, even magic can't protect you. Atlantis at full power probably couldn't defend itself against, say, a gamma ray burst, a black hole pulling the solar system into it's gravity well, our sun going supernova, or heck, the sun just expanding due to old age.

A spell to protect against incoming shockwaves would probably require vastly more energy than a spell that targeted and halted igniting charges. Although ironically it seems much more muggle thinking to halt a theat with through intricate understanding of the mechanisms than to just pump more power into it.