Shredders have always used guitars that allowed great access in the upper registers. That's why you won't see a lot of shredders playing a Les Paul.
Also, when shred first started, it was with super strats, mostly thanks to Eddie Van Halen and his frankenstrat. Ibanez, Kramer, Charvel and Jackson started to market these super strat models and sold tons and tons of these guitars. All of the super strat models were based on the Fender Strat, hence the 25.5" scale, bolt on neck and double cutaway. Things have evolved since then and you'll see more shredders playing different styles of guitars these days but the basic Ibanez RG / Jackson Dinky design remains because it works.
On a personal note, I would add that a 24.75" scale doesn't leave a lot of room for fingers. I have slender fingers and the shorter scale makes it harder to get clean sounding notes past the 15th fret.
I've tried 25" on my flying V and it plays beautifully. Not much of a difference between that and my Fender Strat in terms of feel though...
In the end, a lot of shredder style designs comes from what Eddie and Yngwie used. Even Randy Rhoads went to longer scale lengths after the Les Paul with the 25" Scale Sandoval polka dot V and the 25.5" scale Rhoads V from Jackson. Again, better access and playabilty in the upper registers.