We hauled 4 guys gear on top of a 4 door sedan from Boston to Northern Maine for a canoe trip.
We did the plywood on roof racks thing. I was my friends car, and I got there a day early, as he's not much of a handyman.
He wanted to just lay the plywood on racks, load packs wrapped in plastic tarp, then lash to roof racks.
 I worked commercial construction until the mid 80's, and learned a lot about loading and hauling things.
 I got 4 big U-Clamps, and we drilled and bolted the plywood to the rack. We drilled some 1/2" holes about 6-8" apart, 1" in from sides of plywood and on all 4 sides. We then laced a piece of 3/8" rope thru holes, going over and under, securing at rear of plywood. Then we laid a tarp on the plywood, loaded packs/misc gear,  and folded tarp so rain/road oil couldn't get to packs.
 Then we took some more of the rope , and laced it side to side, looping thru the plywood rope and securing it with a Trucker's hitch, which allows you to really reef the load down. ( If you don't know how, Google it, real easy to learn, excellent for securing camp tarps/tents as well).We repeated this end to end, securing with another Trucker Hitch.
 We checked load at every stop, and it never had too be re-done.
Beauty of a Trucker Hitch, is it gives you a mechanical advantage when you tie it, it's easy to adjust/remove. Having the load lashed 2 places separately is better than trying to use one rope like a lot of people do, and having something shift, which loosens the whole load.
 Laced side to side, and front to back, even under hard braking or a sudden swerve, the load isn't going anywhere
I've seen my fair share of cargo carriers, both commercial/homemade along side the freeway, with the contents spread over the distance the load broke free, and the driver pulled over
 Talk about a bad start too a trip!
 

I'm not sure of the hole size for the U BOLTS, I think we used 1/4 or maybe 7/16", but since there's a plate going across on the threaded end, it didn't seem to be a problem as far as weakening the plywood.
 One thing I didn't mention, the bolts will stick up higher than the nuts, so you want to cut them flush, and hit with file/emery paper, so you don't have a sharp edge to tear the tarp. I also used the self locking nuts with the nylon liner. They're less likely to vibrate loose.
We used a 5/8" exterior plywood. Didn't have a chance that time, but my friend who used the rack for hauling luggage on other trips, put 2 coats of Marine varnish on both sides of plywood when we got back.
 All in all it made a nice rack, fairly cheap, easy to do, and not too bad looking either.

We used one of these, (You need to Login or Register to view media files and links) , on a Prius on a recent trip.  Cut our gas mileage by about 25%.