Without actually listing sales, surely it is currently a reasonable widely accepted fact that the earlier cars are more valuable and more likely to grow in value, and in those cases originality is paramount to achieving a high price. I have heard of any early 240z (non-special edition) selling privately from Melbourne for $100k-ish and going to Japan, and recently saw an early 240z sell in Adelaide for $10k with rust and accident damage that apparently went straight to Japan also. The recent good prices for lightly modified zeds seen on this site are still some way from those dollars.
Because the 260z's are viewed as slightly inferior on a collector level, the glass ceiling that currently applies itself to values allows for things like flares, because of the demographic of the buyer. I think a similar concept would apply to a late 240z also.
There is a level of subjectivity in my post but I'm trying to remain unbiased as possible. I am a bit of a purist (now) but 5 years ago I wanted to buy a 2 seater and cut it up and put flares on it. I wouldn't dare do that to my late 240z now, even though my theory above suggests that I'd get away with it. The market will of course change and I suspect the collectability of late 240s and 260 2 seaters will increase, and as such the price. Eventually, flares on these cars will devalue them as they would an early 240z now. But now I'm speculating, which is very much subjective, but.. history is the best evidence of all.
Ultimately it is the supply and demand and these forces are created by all of us that own and transact in these cars. So each opinion counts towards what is desirable and what is not at any given price level.
To get back on the topic at hand - Mick, I think flares are fine at the moment, but personally I would remove them and weld in new guards if I were to ever sell. If that isn't a viable solution then I wouldn't install flares to begin with.