Re: That's about an inch of torque deflection every three feet or so. That sounds pretty high for high-strength steel.
I don't remember my ship flexing like that, but we were much smaller, and much more ruggedly built and internally braced than a cargo vessel.
War ships are also highly compartmentalized into watertight spaces, not only to provide reserve buoyancy when partially flooded, but so the decks and bulkheads help provide structural support. they're designed, for obvious reasons, to absorb enormous amounts of battle damage.
As for torque flexing of prop shafts, I would imagine that special "twistable" alloys were used in that application so the shafts would not be too brittle and snap under strain.