I lived in the Raleigh area for about a year and a half in 2000 and 2001. Based on your description I'm fairly certain I know the store you're talking about. I will tell you bluntly that because of the shrinkwrap policy I *never* bought a single book there, even if I knew for 100% certain that I wanted it. I bought a few dice there, I bought a mini or two there, I even bought my battlemat there, but when I wanted books I either went to Border's or Hobby Masters. This despite the fact that the store in question was less than a 10 minute drive from my apartment, whereas Hobby Masters was close to 30 minutes away.
So yeah, I'd definitely advise dumping the shrinkwrap policy. To me it just screams "I don't want your business".
I don't have any particular advice for clearing out old merchandise, but if they do decide to have a sale, please pass the word on in this thread. I'm still in contact with some members of my old group, so I'd be happy to let them know. They still play 3.0, so if it's older d20 material your friend is trying to clear out, it might be more useful to them than to others who've switched to 3.5.
As far as getting new stock in goes.... I'm not a business person, but I've often wondered why gaming stores haven't tried out something similar to what I've seen done for new releases on movies and video games. Basically before a new release comes out a customer can put $5 down and be guaranteed a copy on the release date. For customers very eager to get a new product this would usually be faster than pre-ordering online, and it would give the game store a good idea of how many copies of a particular product to order.
One oher semi-related piece of advice. If they do special orders, they need to be good about following up with the customer, whether or not they're able to successfully order the product. If special ordering becomes much of a hassle at all, customers will use the Internet instead.