I have found very few instances that the cover did not allow me to use a trailer hook, when rigged correctly, they cause very few problems. About the only time I do not fish a trailer hook, is when I am prefishing for a tournament. In those instances its better to just see the fish and not hook it, saving it for the tournament. In some cases, if you use a red hook or feather hook, you can actually increase the appeal of the bait with your trailer hooks. Even when the bass are really getting on the your buzzbait and getting the main hook, the trailer hook is a nice insurance policy as you winch your fish out of the cover.
If you do not believe me, how about this. Secret Weapon Lures sells buzzbaits and they feel it is imprtant enough that they include a sharp Mustad trailer hook in the package with every buzzbait. I love fishing, but I really love catching fish! So take the time, put the trailer hook on and start landing more fish!