We can't say Är du överens? just like that, we would have to add something about 'with whom'. If it's several people who agree with each other, you can leave it out, like in Är vi överens?, because then it's obvious with whom we're agreeing (= each other). But just like that, Är du överens? sounds wrong to me. Är du överens med oss? is a good sentence though, but then of course it means 'Do you agree with us?'.
Yes, you can't hear the D from a real speaker either. Historically, it was a TH sound and spelling it with a D didn't change the speech. I Sometimes I see speakers close their mouth as if to make the almost silent D/TH so it kind of affects the next word even when you're not sure you can hear it, in my opinion.