Here is my 2 cents ...
I have been working professionally with computer systems and data networks for about 20 years. In regard to the hard drives: I run external but it's strictly a matter of heat. I keep my PC as cool as possible. Heat kills harddrives ... it's that simple. I run a cheap, quiet external desk fan and three external drives powered by a single power switch. When I want to listen to PC music I flip the switch and it all comes on, the drives appear and away I go. The drives never even get warm as I keep air moving across them at all time. I upgraded my last drive set after three years and never had a single problem. If you’re worried about data throughput USB 2.0 can handle the data stream with about 50% or more to spare. If you really want to obsess about the data stream between the external drive and the PC you can run external SATA and that should make anyone happy. As for noise? I guess one could argue that in the digital to analog conversion it's possible you might pick up noise inside the box but I would argue that if you run any kind of compression you are adding more "noise" than you would ever pick up inside a PC. Most of the higher end soundcards shield the RF and have specs that will give you an idea of their noise threshold. All that being said; if I was going to REALLY get serious as it appears you are (I applaud you for that) I would run the BEST quality, external, USB D/A converter I could afford and get top quality IC's to carry the precious analog signal into your system. I believe there are several posts regarding these USB D/A converter devices in the archives. Don’t worry about the digital side for the most part it's immune to noise. I wouldn’t run ANY sort of compression – this means you’re going to have huge files and that equates to big drives. I'm sure you know this.
I don’t worry about redundancy of the data as I have the music on CD and can re-rip if I ever have a catastrophic failure. If you need to protect your data … that opens up another can of worms. If I needed redundancy I would possibly consider a data network and run a drive array with some sort of RAID system. I would keep this array in a separate box. The stand alone RAID boxes are often referred to as a "NAS" boxes. Buffalo Technologies has one that will do 750 gig with RAID 5 protection for about $900 I think. This solution gets expensive and requires a moderate degree of technical expertise. I guess DVD media is pretty cheap. You could always burn off any data you wanted to backup to DVD.
I will tell you what I tell my clients - cover your back-side. PC's (and Macs) hate people and they will fail at the worst possible time.