Leave the audio untouched. Just rip using makeMKV and that's it for a 1:1 copy.
It depends. If you want to be able to play the movies from multiple points in the home, than a NAS would be the better option. If you are only going to be playing from a single point, than external HDD's would be better.
If you go external, it's going to be expensive. You'll need a multi-bay enclosure with multiple large drives. Not that a NAS with enough space wouldn't be, but I have more experience with former than the latter.
With minimal googling you end up with something like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16817198060
Now according to the spec's this will handle up to 6TB's for a total of 24TB's. Which gives you about 530ish movies at 45GB's/movie or 1600 movies at 15GB/movie (roughly what handbrake yields with minimal compression if memory serves) or 3000 movies at 8GB/movie (more aggressive compression, but still with minimal quality loss depending on the movie). Now you can see what a difference doing a little compressing can do to your storage needs.
It's late so hopefully my math is correct. In either case you get the idea.