Up until this project I've not used scan data when direct modeling. We have used scan data and then converted to surfaces with programs such as Gemagic. This works, but has some pretty big drawbacks. It is much better and cleaner to create a model directly within your CAD software.
With the Bess, we scanned everything in, but I only use it as a guide to create profile shapes, section shapes etc. It can be really helpful with cross-sectional shapes. Again, these shapes are just used as a reference and then drawn out directly. Prior to using scan data in this way, I used measuring and photos much like you have described.