Honestly, if bacteria had human intelligence, I don't see why their naming system should differ that much from ours: just pick names that you like. They don't all have to be unique, especially if they're the type of bacteria that don't really move much. If you want to be named Bill, who cares if there's already another Bill who lives a centimeter away? You'll never see him...
And even if they do move, they'll just distinguish one another the way we do: by personality and connections and what not. "Oh, Vanessa? Do you mean the one who hangs out by the epithelium who likes rock music, or Jane's sister Vanessa?"
The thing is that bacteria as they are now kind of go wherever they want and can potentially come into contact with millions of their brethren over their short lifetimes, which would make naming a hassle. But if they literally have 'human' intelligence, I'd assume they'd start acting the way humans do: hanging out in cliques and smaller groups; establishing families, within which they really only need to know each other's names.
I mean, there are billions of humans on the planet, but you don't worry about potentially running into someone with the same name as you, do you? No matter how likely it is. If they're outside of your social universe, it's really not your problem. And if they exist inside of your social universe, you'll figure it out. After all, you're not the same person.