Yes, gods can recognise each other because through their eyes, they appear as columns of fire and cloud. Case in point is the birth of Dionysus, as Hera saw through Zeus's mortal disguise while he was in Thebes dating Semele. To all he appeared as a rich prince, but to Hera and other Olympians/Titans (Calypso is the daughter of Atlas the Titan from your question) the mortal disguises are nothing.