Tricky to answer, I think.
My personal preference is for `vintage`, in `as flown` condition - scars and all!
However FSX is a `today` sim and the fact is that modern flying requires modern avionics as a requirement, not a choice. No B-17 would be allowed to fly unless their radios met current requirements, they need a transponder, and no pilot would be daft enough to take off in a Spitfire for anything other than a local flight without at least a hand-held GPS (and often these days a real-time weather package).
Primary safety and the longevity of the aircraft is the prime consideration, not pretending its still WWII. And I fly them in FSX as if they were delicate antiques, not "fly `em, fight `em, throw `em away" mass-produced short lifespan tools with a service life of weeks or months, not years or decades.
So, for me at least, there IS a prima facie need for access to modern avionics. And I think the popups provide the answer - they don't clutter the VC and change the original look, but they are there if needed.
But having the choice is far and away the best choice!