The down side: UV exposure to hoses and OEM coolant reservoir. I think your engine hatch/bonnet may rattle because the cover is missing. The inside of the hatch will get dirt quickly and will require cleaning more often.
The up side: when you have a radiator hose burst, you will know instantly.
Yes, when the body flexes, I hear a creaking sound coming from the engine hatch because it no longer rests on the lip of the engine cover. I've wanted to add rubber stops to help, but haven't found a way to integrate that as of yet. It does not bother me at all.
I've also noticed some of the black hoses that came with the Comptech Supercharge kit starting to turn gray on top because of the UV. They are the type of hoses that have a cloth outer layer. The car's not in the sun that much either. I plan to cover those hoses with some corrugated split tubing.
I have not seen any changes in the color of the OEM hoses, but the UV has to take a toll on rubber. The question I would pose is, how long does it take for the UV to effect the type of material we have in our cars, and does heat, out gassing, and ozone effect it in the same timeframe. Rubber hoses go bad... period. The question is; does the UV accelerate it significantly? Additionally, I would not use Italian sports cars as a measure of longevity. It has always seemed (to me) that the material in Euro cars breaks down rather rapidly... UV or not.
I changed the coolant tank to a polished stainless steel billet version... looks a LOT better. No issues with that.
I don't notice the inside of the hatch getting dirtier faster, but that may be because I clean both sides of all the glass every time I wash the car... which is often.
If a radiate hose bursts in the engine bay, I don't think it matters if you have the engine cover is there or not... the engine bay will instantly fill with steam and the engine cover will not prevent the steam from rising above the engine cover. The engine cover does not form an air tight seal. The steam will be billowing out of the Rear Window Garnish in either case, so you will definitely see it and have poor visibility out the back.
More heat will hit the tint film, so that could cause potential issues. Then again, tint tends to pop off the glass over time anyway. Hard to say for sure.
I also forgot to mention, without the cover you may get reflections from shiny parts in your engine bay in your rear view mirror.
I question the "more heat will hit the hatch" idea. Here's my thinking... Most, if not all the heat from the engine and exhaust headers are transferred through "convection". The heated air definitely gets to the top side of the engine cover where there is no vent for ambient air to enter like what the engine bay has. I also can't imagine that "radiant" heat (mainly from the exhaust headers) would be that great since there is not a direct line of sight to the hatch (perhaps a little reflection off the firewall though.) To me, the Sun would be a much larger factor when it comes to radiation, and, of course, the engine cover doesn't matter there.
I definitely get glaring sunlight reflected to my rear view mirror at certain times when the sun is high. It mainly comes from the Comptech strut bar and reflects off the underside of the hatch glass.
I took my engine cover off because 1) I have some nice goodies to show off, and 2) reduced weight by 25lbs.