It would miss in Gen 5 (or prev Gens), but after that, nope
In Generations 1-5, Whirlwind has 100% accuracy (in other words, it is affected by Accuracy and Evasion stats).
From DB's page on Whirlwind, so as you can see, before Gen 5 it would miss, as it had a defined accuracy. This would mean that it can miss in Sand directed on a Sand Veil Pokémon also.
But, after Gen 5, it had it's accuracy removed, and so, it won't miss now.
I also checked it through a battle. Chomp's ability was Sand Veil, and Hippo's was Sand Stream, and when Hippo used Whirlwind, it missed as Chomp had Veil.
Hope I helped!