I don't think you're going to hear that much of a difference between the analogue connection and the optical connection in the Airport Express. I have several ways to get Itunes to the same AVR and I can't tell the difference between the different DAC's. The analogue connection in the Airport or from my Ipod on a dock. I use the analogue connection so I can use it on Zone 2 or Zone 3. The only thing I don't like about Airplay is how unstable the connection can be. Some have reported that the connection can drop and that firmware and app development is an issue with some AVR's. I never have a connection problem with the Airport Express.
As far as optical inputs they are all the same no matter how expensive or cheap the AVR is. The same goes for a DAC. If a DAC in one particular device does have a different sound it's flawed. The DAC is supposed to be transparent and not color the sound in any way.
I think you should stay away from B&W speakers. Not that they're bad. Many of their speakers have large impedance dips and can't be powered properly by the AVR's that you're looking at or in that price range. To be safe you need a 4ohm stable AVR with B&W speakers.
For AVR's I would look at Denon, Yamaha, Pioneer, and maybe Marantz. I'm a fan of Onkyo and own several but I would stay away from them now. Their products have really went downhill in the last couple years. I won't be buying another Onkyo if this trend stays. So I won't recommend that you buy from Onkyo either.
There are a lot of other book shelf speakers choices. Polk, HSU, Bic America. For what you're looking to do I would start with 2.1. Two mains and a subwoofer. Then add a center channel later. So for now that's three speakers. The center channel would be the fourth.