It's a myth that the gods had compartmentalized domains. You in fact find dozens of gods to pray to for any given thing. If you wanted protection against the seas, you'd actually pray to Ino-Leucothea, Melicertes-Palaemon, Achilles, or even (and especially) Aphrodite.
The gods do not have domains. They have powers, and you pray to a god for their powers to help you in whatever venture you have.
Sure, some gods are more associated with activities, but again, these aren't compartmentalized in any way. Hermes is most commonly associated with travel, but if you wanted protection through xenia, you'd also make a sacrifice to Zeus. You certainly find inscriptions where multiple gods are addressed for some activity.
And it's not even individual gods. Sometimes, it's individual aspects of gods. Robert Parker, whose study On Greek Religion (Cornell: 2011) is a great, updated summation of the topic, make as much clear:
It was common in oaths for a single god to be several times invoked under different epithets; oracles would very regularly advise cities to add a cult of a god under a new epithet to their existing set of cults of that god; and in a famous episode Xenophon, regular worshipper of Zeus Basileus, was told by a seer that his financial problems were caused by his neglect of Zeus Meilichios. Even if in one perspective Zeus Meilichios was simply one aspect of Zeus, in another he had to be treated as an independent figure. He was often portrayed differently too, as a gigantic snake.
These different "aspects" of a deity shows their branching specialties:
To take an easy example, Aphrodite is not just the patroness of sexuality but also, as “Aphrodite of All the People,” a source of civic harmony, and, as “Aphrodite Fair Voyage,” a friend to sailors. As wife/cult-partner of Ares, she even has a certain relation, which is apparently not merely one of antithesis, with the world of war: in 480 BC, for instance, the women of Corinth are said to have prayed to the goddess to inspire in their menfolk “desire [n.b.] for battle against the barbarians.”
Structuralists have looked for a "unifying principle" embedded in these activities. So praying to Aphrodite so that men "desire for battle" calls on her power over desire, which is clearer from her sexual powers. Even this is a bit too simplistic, and Parker finds it difficult to naturally see "Why does Zeus, if his characteristic mode is sovereignty, watch over the household stores, in the form of a jar, as Zeus Ktesios?" (p. 93). Explanations for these activities would be ad hoc.
Parker doesn't give a real conclusion, but rather lets the gods just be gods: they have powers, they take up different domains, these domains are absolutely not specific to a single god, and the way they develop is sometimes a mystery and rarely a necessity. This is a more naturalistic explanation for the gods' powers: they have the powers because their worshippers attributed those powers to them.