As others have explained, the "S" stamped scarves are those purchased at one of the Hermes sales. There are a few venues that have scarves at the sales, including Paris, NYC, Beverly Hills and sometimes Toronto. I am fortunate to have several scarves from various sales - yeah, they are 40% off. Sometimes they are marked with the "S", sometimes not. Cashmere GMs purchased from sales frequently do not have the "S" stamp on them.
To me it is extremely important to know if a scarf was purchased at a sale or not because in fact, many of them have imperfections. It is unfortunately not true that they are all in pristine condition at the start of the sale. The worst I have ever seen is when the scarf somehow slipped during the silkscreening process and the images were doubles as if viewed with one's eyes crossed. Most often they are small runs or something like that. The "S" themselves can be a problem, many are ever so lightly stamped on, some are smashed onto the fabric of the scarf and show through to the "right" side.
I don't care if a scarf is purchased at a sale or not. If it was, I would like the price to reflect that, but if I really, really want the scarf, I don't even care about that. I do, however, want to be sure that a sale scarf was purchased by someone who is aware that they can be damaged and who will therefore have (hopefully) looked to be sure that any flaws are minor. There are some buyers who don't want to have a sale scarf under any circumstances, so the fact of the "S" stamp can affect the re-sale value, as others have noted.
I also agree that it reflects on the credibility of the seller. I once purchased a scarf from a fellow collector who deliberately did not include the information in the auction - I will never buy from her again. She often goes to sales and never mentions that the goods she sells on eBay were purchased at a sale. Some will say the item is new and unworn, thereby attempting to obscure the fact that it was purchased at a sale. I prefer to deal with people who are honest!