I know a bit about it from when I was living in Tokyo... I never went to a show because I was too busy but I did have a little look!
You can look up the theatre schedule on their website and plan to go when there's a show on, and you'll be able to go up the elevator to the 8th floor and see everything - but you can't go inside the actual theatre unless you have tickets. I believe they do close the floor off to people who don't have tickets for certain popular shows like graduations and stuff maybe.
They sell goods on a different floor in Don Quixote, I think it was the 4th or 5th floor.
As for theater versions of CDs, I think back in the old days they did physically sell them at the theater but nowadays you can only order them online.