My first thought about these is that Oda decides not to to stick with Greek Mythology or Roman Mythology. Pluton which seems to be a direct referance to Pluto the god of the underworld in Roman Mythology and Poseidon who is the god of the sea in Greek Mythology. This seems to be a reference to how the Romans took on a lot of Greek ideas and changed their name, Hades being the Greek god of the underworld, so is that saying Pluton is a more updated version of the ancient weapon Hades?
I do think however that their names have some relevance to what functions they have. Pluton we know is ship, but I think that its reference to the Roman god of the Underworld gives a hint to what the ship is used for, Death. Poseiden I think is also a ship, actually a submarine, named after the Greek god of the sea I think it would be only fitting.