You may hear otherwise, but I've been stalking NA-T classifieds for about 10 years now and from my experience, you'll get a substantial chunk of your money back on the conversion, at least the main components. A £5,000 whifbitz na-t kit would definitely add 3-5k of value to the car, and no, people definitely don't still view it as an NA Auto. Labour costs and all the auxillery things you'll inevitably have to do once you start (that really snowballs the price of the conversion) is a different matter, and somebody with actual experience doing one would have to answer. There's a lot of benefit finding one that's already been converted, and all the headaches/issues have been chased out, I'd definitely pay a substantial premium for it and I'm sure others would too.
Once you reach a certain point of collectability, if your car is a very clean example etc, you're attracting a different crowd who definitely wouldn't pay more for a converted car. So all depends on which audience your car is targeting.