I was shopping for mowers earlier in the year and noticed that the mowers sitting outside had a significant amount of rust on the top of the engine beneath the debris shredder, and this was with a hood on. I know that most engines have an alternator beneath the cover. Assuming that you only cut during dry conditions and still keep the area clean with a blower/air, it shouldn't be an issue. If you allow any water to get in there, you may encounter problems years down the road. Maybe you won't, but consider that the manufacturer engineered the mower to run both adequately and efficiently with the hood in place. My cub cadet actually had an air dam built into the hood which brought air in from both sides to the top of the engine.