The Hydra doesn't appear to have much that could take down Acnologia aside from its poison blood. I'd say Acnologia has the skills and abilities to kill the Hydra, though it won't be easy thanks to its regeneration.
Correct me if i'm wrong but doesn't the Hydra have the Ap and durability advantage which if true makes Acno's only way of winning this fight, inflicting more damage than the Hydra can regenerate, very difficult to achive. Furthur if any of the Hydra's blood gets into Acno's body (or onto his body given that Herc's hydra blood arrows can kill people with much higher dura than Herc has AP) he will die in agony.
Hydra for reasons above along with the enviroment making it more easily for the hydra to land direct poison attack or an attack that would leave his skin vunerable to poison at Acnologia, which will be the beggining of the end for the poor dragon.