There are some anime with Nephilim. Senki Zesshou Symphogear G is one.
Others touch the subject as half angel half human. And the rest don't call them Nephilim per se but they do follow that concept.
And no Zeus, titans, and hercules were not Nephilim. They are from a completely different mythology.
If you want to still somehow mix both mythologies then only titans would apply as a Nephilim.
If you are only thinking of giants being the ones in control before the human era then there are even more anime with that subject but they were not called Nephilim. Anime and other media are inspired on multiple mythologies and cultures so you can't really call all giants Nephilim.