We know that when Hydaelyn was summoned, her summoning was very different then Zoidark's summoning in one key area. Hythlodaeus tells us that when Hydaelyn was summoned, it was her own summoners who died to "fuel" her. When Zoidark was summoned, his summoners sacrificed other people to "fuel" him. So Hydaelyn was way, way weaker then Zoidark initially. It's been speculated that part of why Hydaleyn Sundered Zoidark was to make him more equal to her in power so she could deal with him. There's also a good chance that Zoidark was influenced by the people dying to fuel him who might not have known what the Concept behind Zoidark actually was. The people who died to fuel Hydaelyn were the very people who came up with her Concept, so the odds of her Concept getting influence by some other desire is a lot less.

Emet-Selch also says that Hydaelyn and Zodiark fought for a long time over the Planet before Zoidark was Sundered. So I'd say the Ancients did know about both of them at one point.

Amusingly... you can find the halos behind Zoidark and Hydaelyn by themselves in the Acadima Aydenar. They are the same halos that are behind the Zoidark statues. Which suggests Zodiark (or at least the form of him) was something to the Ancients before they summoned a Concept based on him.