First, a LBS cannot sell a Trek (to pick one) on-line. The companies do not permit this. You can't surf the net and look for a deal, then buy the bike on-line and have it shipped to you. So most of what you've said regarding this part is commentary.
Second, I work on a top 50 shop and we do about $7 million in bikes and accessories a year. We have a website, and people can order parts, clothes, etc on line, come in and pick it up (if local) and not pay any shipping. If they want, we can ship to them. The catalogue and web presence is extensive as are the ones for the bigger shops I've looked at (take a look at Mellow Johnnys for example
http://www.mellowjohnnys.com). Our inventory moves rapidly. Last Saturday, in three hours I moved four road bikes for close to $9 grand in bike sales alone. We can do $60 grand on a good summer Saturday, no problem. So not every shop is as you assume.
We do have an inventory list. This shows all bikes. I cannot tell you how many times I've had a customer tell me they saw a bike on line on Friday came in on Saturday and it's gone. I really wish we'd do away with that.
We had Performance open near us. Our sales went up. I sold two bikes to customers who had purchased there, returned the bikes and came to us and spent more money.
Not everything is as it seems to the observer. BD serves a certain type of customer. If we get someone in the store that's considering them for their purchase, we rarely lose the customer to them for a lot of reasons. It's kind of humorous to watch the process of the customer bringing us a bike to build in a Motobecane box and they begin to add up the "extras" and it's not as great a deal as they imagned. Hardly anyone I've seen buys from them that's a mechanic and can handle the bike themselves. We take really good care of those customers because they figure it all out and buy the next bike from us.
In a couple of cases we've done fittings for BD customers and it's not the right size bike. Ship it back, take it apart, etc...
It's another distribution method. We just deal with it and generally we get a new customer when it's all said and done.