I have to say that the thought you have is valid to a point. If you can walk in and get Timmy, Marcio, whoever to design and shape you a custom board that is great and you should do it just for the experience alone.
What happens to most shapers that have a decent size biz is that they have one or more trusted and experienced backshapers (ghosts) working for them to help keep up with demand. If you do it right -and I hope that I have- you first have your design files dialed in as close to the desired finished board as you can so that all the main characteristics of the designs are already in the cut blank. Then you work very closely with your shapers to teach them how you want your boards to come out. The rocker and bottom contours are very difficult to screw up, but the biggest part of the boards that they are tuning in is the rail, so that is what we really focus on perfecting. In our Oceanside factory I have a "Master Shaper" who looks over any other backshapers' work and makes sure to keep them tuned in and on track to what I want. We don't hire just anyone to shape for us- my guys are all amazingly talented in their own right, and I am lucky to have them making our boards.
I regularly check out our boards at shops and in the factory to make sure they feel like my own shapes.
To make it clear how much I trust my crew (not just Oceanside, but around the world) I get them to make my own personal boards whenever I am traveling so that I am riding exactly what our customers are riding too.
As for our files being used by other shapers - We have our own shaping machines and keep things in-house to avoid that sort of thing, and I will only work with people that I trust anyway. I am sure someone has managed to get their hands on my files before, but I can't get all worked up and worried about a couple of boards here and there. We also can pass-lock our files so that they can't be used by people outside our groups.
Hope this sheds some light on the topic...