Whis and his dad are not gods. And Zeno is something beyond a god.
I think the accepted interpretation of his statement is that he killed all 12 of the Kaioshins. Which in turn would kill all 12 of the Gods of Destruction.
None of the gods, not even Zeno, seem to be omniscient. None of them know what's going on in other universes unless they happen to be visiting one at the time.
There's really nothing preventing Zamasu from showing up in a universe, immediately killing the Kaioshin, taking the God of Destruction with it, and then moving on to the next. Once the gods are all dead, he's free to exterminate mortals at his leisure.
We don't know that the Super Dragon Balls follow the same rules as the Namekian Dragon Balls. They might not be reliant on the life of their creator.
As for who created them, it was someone named Zalama. They told us that much when Bulma asked that guy to tell them everything about the Super Dragon Balls.