"Can the non-functional vents on the kits be made functional?"
Sure they can, it all depends how much time and or money you want to spend. I always thought all the ducts should be functional, especially the brake cooling ducts. People invest big bucks in 14" rotors and then have fake cooling ducts that are just creating wind drag. Actually as originally designed the GT40 has a very intricate cooling air duct system, most of the kits don't replicate this as it's not very cost effective.
Fiberglass is not that hard to work with it just takes a little research and time and patience. You can make forms out of cardboard, styrofoam board, foil and foil tape. My "kit" didn't come with any duct work so it's all being fabricated from scratch. The front brake ducts go straight up the side of the chassis to a flexible 3" duct hose that connects to the brake backing plate. Unlike the originals which turned into the chassis and back out to the backing plate. The front brake and NACA duct vents all have connections that allow for the front clip opening.
Another place that causes problems is the spare tire cover radiator vent nostrils. On the originals the air passage through the radiator is totally sealed, all the air that comes in the front goes out the top nostrils. If it's not sealed or if the nostrils aren't shaped properly the front clip can become pressurized and cause wind drag.
The front side NACA ducts go to eyeball vents on each side of the dash and the center one goes to the defrost vent. The large side vent at the back of the doors splits at the vent entrance, 2/3 goes to the rear brakes and 1/3 goes to the engine compartment. The upper side vents behind the doors obviously go to the intake but this is another area some kits fall flat. The intake area has to be sealed so all air coming in these vents goes to the intake. Otherwise the intake gets hot air and the rear clip becomes pressurized also creating drag. This is difficult because it has to provide for the clip opening just like the front.
Pressurization of the front/rear clips has caused other problems. Front spare covers have been known to blow off and even possibly rear clips if the latches are substandard and the pressurization lifts the clip enough for air to get under the front edge.
If your really serious about this you need to find an original car or one of the better kits and take some pictures, believe me you won't remember how everything goes.