DVD quality - not much can be done! It's because the MacMini is connected via HD, the BeoVision 9 is expecting it to be an HD signal and therefore doesn't upscale it. It's the MacMini which is doing the upscaling, and it's not the best upscaling, especially on a 50" screen.
Video quality - simply because the iTunes Music Videos are meant to be played on a little iPod screen, not the best 50" TV in the world!
Storing DVDs - you'll want the app Handbrake, and use the 'Apple TV' preset when ripping. You'll get 5.1 audio and very good quality video. I've upped mine to 3000 kbps instead of 2500 and I'm using 2-pass encoding - takes a very long time, but it's worth it.
Standby - not sure about this, best to speak to your dealer.
AV socket - No.
You only meantion BeoLab 9s and a BeoLab 2. I assume that means you aren't running any rear speakers? Definitely worth the upgrade IMO, especially with being able to rip DVDs with 5.1 sound!