actually most of the time the wires get ran inside the inner structure so they dont get pounded with debris.  an engine bay wire tuck is just like the wiring inside of the vehicle.  you dont want wires running all over hell creating a cluster f*** inside the vehicle, therefore the wires are all loomed and "tucked" behind the dash and behind interior plastic panels.   there is hardly ever a time when i have had to mess with wiring in the main harness behind the dash. so with that being said i guess the basic concept to an engine bay wire tuck, would be to create the same clean look that the interior of a vehicle has.  i do agree that diagnosis of a wiring problem could be difficult, but when doing a tuck you are basically building a brand new harness. so if it is done properly there should'nt be any problems to diagnose.