I make holsters with both and here is a run down on gun wear...
Does kydex cause wear marks or mar the finish of stainless steel finish? Is is more harmful to SS finish than leather?
First of all yes Kydex will wear harder on a gun's finish. Leather will wear on it too. Think about it, leather strop barber's razor.
With that said let me give some advice and maybe dispel some misconceptions about holstering a gun. First of all if you have a safe queen DON'T CARRY IT REGULARLY in any holster.
I suggest to most of my customers that have very expensive handguns that they only carry them for special occasions or suffer the consequences. It is best for daily carry to carry an old beater that is reliable but something you are not going to have a fit if it gets scratched.
With that said another thing I see is suede lined holsters. All suede is chromium tanned and under the right conditions the chrome metal from the tanning process will react with the finish of a gun. This is more a problem with a blued gun in high humidity than other finishes and stainless or nickel is less likely to be affected.
For most of my western holsters I line the inside with veg tanned leather so the inside of the holster has a finished side of the leather against the gun. I do this mostly for appearance but I believe a smoother surface will less likely attract dust, dirt, and other abrasives. Remember that a barbers strop is usually rubbed down with a jeweler's rouge to get it to sharpen. With that said the best thing you can do is to keep your holsters clean inside by blowing out any accumulated dust or dirt.
There is no perfect material that I have found that will absolutely guarantee no wear on a gun's finish if it is carried daily. Besides that you will be bumping the gun into to stuff and rubbing it against things no matter what you do when carrying it on your belt.
A shoulder holster is probably the best option for carrying in a protected way. But as far as linings and materials go just plain cow hide will be your best option.
I have heard that horse hide is better as far as gun wear goes but I cannot speak from experience as I haven't run a side by side comparison under controlled conditions. Remember that a lot of what you hear is just stuff that someone has convinced themselves to believe in without any real proof.
Moral of this story is if you can't stand a scratch on your gun then don't carry it unless you are willing to have it refinished from time to time.
BTW: It is not that much work to take some wet or dry 800 through 1500 paper and polish out a stainless gun unless it is bead blasted then ... well get a bead blaster and a compressor...