If he knew Tonks through Sirius, wouldn't have dropped out of her life a long time ago? Like, when Sirius went to Azkaban?

As to the name thing, when my cousin went from Joey to Joe, and my friend Iffer went to Jen, everyone respected their wishes and called them by their preferred name. To insist otherwise would be *rude*. I can't see how Remus Lupin gets a pass just because he might have known Tonks as a little girl.