Briefly, yes. Zynga's Café World and PlayFish's Restaurant City uses Away3D.

I think developers might use more of 3d engines because 3d is not everyone's cup of tea - they can just focus on implementing game logic and mechanics instead of meddling with math. However they would shy away from game engines like Flixel, for reasons that Nick Wiggill has mentioned. (eg. risk of middleware)