In the final episode of Nadia of the Blue Water, Captain Nemo reveals to Gargoyle that there are no more Atlanteans, and that he (Nemo) is the last one. But Nemo has a daughter; Nadia, and he may or may not have made Electra pregnant. So how can he be the last of the Atlanteans?
From what I can tell, you are correct in saying that Nemo is technically not the last of the Atlantians. The most logical reason that I can think of for him saying it is that he was the last person to grow up and experience the Atlantian traditions and society. Because Nadia grew up as an orphan who didn't know her background, she didn't have experience with that society. The society was gone, so Nemo was the last person who would experience that society.