"How does the (sub-sonic) artillery shell get through the flight deck, "
I think you'll find that KE rounds fired from tanks can hit 1700m/s or about M5.
The challenge is to build essentially a cup that acts as a 1 shot gun barrel to contain the propellant load long enough to accelerate it before it disintegrates with the drone (or at least the shell) pointed at the deck.
I think a M5 Tungsten Carbide or DU sabot will go through any steel deck thickness a carrier could reasonably carry. There's a lot of deck to cover and every mm extra adds a serious amount of weight.