http://www.numismaster.com/ta/numis/Article.jsp?ad=article&ArticleId=13569 This article predicts that the value of the 1946-S quarter will rise in the future (the article was written in 2010, so it is the future and it hasn't happened yet...) but doesn't go into details why. Is there anything extraordinary about this coin other than it had the lowest mintage since the 1940-D at 4,204,000. Does this guy know something the rest of us don't know? I hope he's right because I have a nice bright white PCGS MS65 specimen.
He was speculating on the coin for the reasons you stated. No doubt it will go up, in time, and I'll wager he didn't give a time frame. I didn't take the time to look at the article as I've seen too much of this but it makes for a nice article.
PCGS has 3500 1946-S's in MS65, by far the largest Population in 65 of any Silver Washington, more than half again as much as the next nearest (1947-S at 2277. This should be the cheapest silver Washington in 65. To me, that article is pure clueless clickbait at best, and representative of a vested interest - name an "expensive" coin issue with that many examples in MS65 - at worst.
As has been said before, survival rate is a major component. In the case of this coin (like so many others), it seems the lower mintage will hurt its value in relation to other quarters from around that time. People must have seen the low mintage and hoarded them. Hence the high(er) population in MS65 or greater. This ran across my mind also. Create hype to unload stash. A strategy as old as man.
Which negates the premise of the article. Let's compare the (PCGS figures) 420,000 estimated survival of the 1946-S, including 3500 in 65 and over 1900 finer, with the 1955-D of more than a million fewer minted, estimated survival 318,000, 870 in 65 and 256 finer. Which issue deserves that article more?