Confusion about "would it not be better if" vs "it would be better if"

This happens to be an idiom which exists almost identically in German and English, and it works just the same way. You can rearrange your friend's statement to match the German style to make it obvious:

"My friend asks if it would not be better for you to come here."  
"My friend asks: would it not be better if you came here?"
                 Would it not [be] better if
                 wäre  es nicht    besser wenn

If someone says "Would it not be better if you came here?" or "Wouldn't it be better if you came here?" they are saying that they think it would be better, and they are asking you if you disagree. The 'not' is a bit confusing, because it doesn't invert the meaning. If someone says "Would it be better if you came here?" that means the same thing, but is a more neutral/open question.

Well, "would it not be better if", is used in the context of comparing with something implicitly. The other something generally is the opposite of what is proposed explicitly.

So, it means that your friend thinks it would be better if you go to his place, rather(implicit) he coming over to your place.