The game lists them as creatures, not NPCs, so they have white souls like every other creature.
Lore-wise, though... I'm wondering that myself. The most believable reason would be that after centuries of being enslaved and drugged the Falmer degenrated and became mindless, bloodthirsty creatures rather than a sentient mer race. They can't even speak anymore and live in primitive tribal structures.
Keeping that in mind, I still don't believe it should turn their souls white. They used to be mer, they still have the potential to regain what they lost. Centuries of blindness and savagery shouldn't be enough to overshadow their elven ancestry...