depends on the shop. I know builders that just do what looks right and make it right after its built. There are also builders that spend tons of time getting everything perfect trying to find the best handleing most efficient, fastest hull out of their contraints. A lot of builders are doing scale tank testing, some doing wind tunnel testing. Stevens has a large tank testing facility and a phd program in ocean engineering i'd like to take someday which focuses on hydrodynamics as well as others.
when i worked at viking, they did tank testing on the new 74 at stevens. Cabo also does their testing there. For some cool pics check out
http://www.wallypower.com/ pics 37 and 38 under power 118