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They may look similar but they're not related one bit. Yellow hails from Kanto, Bonnie hails from Kalos. Two distinctive regions and two distinctive characters. Yellow is much older than Bonnie too and although it would raise an eyebrow if they happened to be related, the odds are so minuscule that its not even worth exploring.
I don't think so, I think the only similarities they have is that they are blonde short girls that love Pokemon. I don't think they are related because those are pretty common traits that can be share between people who aren't related.
I don't think they're counterparts either. Yellow is more of a typical cleric character as she's shy, caring, and she doesn't really like to fight unless they have to. She even has the ability to heal. While Bonnie is more so an excitable and curious child.
It's probably just a coincidence. It's not like Yellow has a particularly unique appearance that makes any character that resembles her automatically related in some way.
Plus even appearance aside it's not like there's any connection between the two. They're very different.
Yellow has the power to heal pokemon and understand them telepathically in the manga. Bonnie cant.
Spoiler:
Not to mention, Yellow hides her gender because Green wanted her to stay undercover. Idk if she still wears that hat after volume 7 to make her look like a boy.