I have been running my deuce with the right side hood panel off for thousands of miles and have some experience here.
It was removed to provide space for the deep water fording components, the crankcase breather tube, in particular. Removing it for fording also lets the water from the fan out as shown in the image below.
At standstill, when the engine is producing a minimum of heat, it will take longer to warm up, perhaps 5-10 minutes more. Now, with the wintercover, it warms up pretty quick anyway.
When you are on the road, it makes very little difference, may even be an advantage to keep the engine air filter canister cooler (=better performance. Most big trucks have the airfilter outside the engine compartment).
In the winter when we expected snow, I put a piece of plywood over the side when the truck wasn't used.
Before the Greenville, KY trip last month, I modified the hood panel and installed it again. It needed a small cut-out for the, now permanent, crankcase vent. The vertical pipe supporting the air intake pipe/mushroom also serves as the crankcase breather vent (from the crankcase vent filter).
