FYI, Velvia 50 is NOT discontinued. It's only the US distributors who keep saying that, maybe it's officially discontinued in the US but they're still making it in Japan.
I just bought a pack of the *new* style box from this guy in Japan, it rocked up a week later in aus, and yes, it's the new package, as is the 5x120 I bought, both exp Jan 2015.
But man, look at that price (still, a sheet is cheaper to buy than to process it around here).

As for the OP, I think you answered yourself. I've read the story that when they released v100 (or 100f, can't remember), that it was meant to "fix" the problems with the v50 (discontinued original). So many people complained that they brought back the v50 (this is back in 2006 or so). But they still love their 100 versions, so they produce it by the truckload. But it doesn't sell as well as the 50, so shops just have more and more stock. It's also a buttload cheaper than the v50, noone wants it.
Honestly, for most people who scan, it doesn't make much difference because you can adjust Sat etc in photoshop.
But Stone, you sound like me, I've heard you say you hate photoshop, I don't even have it (I run linux). Scan and print and nothing in between (maybe crop). Hence I buy my v50 too. But I do also have some 100 and 100F in the freezer that I use on occasions, depending on how 'special' I think the shot will be as to what film I want to waste on it.
I've still got 18 sheets of Quickload Astia in the freezer, I used my first 2 frames for a portrait of my gf and her grandmas at her 30th, I'm saving the last 18 sheets for something as special.
Similarly, the v50 I save for those 'spectacular' sunset-landscapes, the v100/f I use for just regular midday shooting and ones where I may get a good shot or may not, so don't want to waste the v50.