I think it would depend on where the chunk is missing. Trailing edge wouldn't bother me too much since it already has a hole for the shaft...ok it would and I would fix it. The leading edge would bother me more since it would act as a scoop. This would effect the economy. It could also cause the tunnel cover to break off.
I think the question that should be asked is... what are these covers for? There has been some discussion in previous posts, that the covers prevent cavitation. I discovered that one of my covers were not attached well, but I did not know about it until the boat was hauled. I just had it re-attached and will see if I notice any difference.
The covers smooth the water flow over the hull bottom and keep turbulence out of the props. That is a long way to say "Reduce Cavitation".
Can you run without them? Yes, but they were designed, manufactured and installed from the factory for a reason and I personally would keep them. If you have a chunk missing, have them repaired. Any good fiberglass person should be able to repair them for less than the cost of new ones. The other issue is finding new ones. Older modes that have been out of production for a while are going to be near impossible to find.
I had one missing on my 1998 31 open and bought it from Tiara who still has the mold $500.00 later a few screws and some 5200 and its on.Will see how it effects the boat after we get it back in the water.
One comment to keep in mind. 3M's 5200 is one of the best products ever made. But, It is my opinion you never want to use it on anything you may need to take apart one day. You will need a chisel. Their is a chemical called DeBond to help soften it but this removes about 1/20th on the bond at a time and takes forever to work. I would suggest you consider 4200 as an option.