A company I worked for a few years ago operating Aero Commanders the company procedure was to have the cowl flaps closed all the time. If you needed to open them for overheating there was something wrong with the engine. I operated them from Melbourne to FNQ and no problems with temps!!
The company owns approx 40 aero commanders now with no problems having cowl flaps closed. The boss is an aircraft engineer who Rockwell go to have questions answered on the aircraft they built and designed.
Anyway just one type of aircraft/engine (lycoming IO540) from memory.
Non turbo so that can make a difference to whether they are needed.