As one who did the flying to get several of the sims certified in the UK, I can probably say with some certainty that you can use the sims to learn to hover. It's a question of how the instructor does it, just like in the real helicopter.
I had the manufacturer set up a special area for teaching hovering, with lots of vertical cues, and it really did make a difference in teaching someone how to learn the basics of hovering.
There have been several people who have spent considerable time in the sims and then gone straight out and hovered nearly perfectly.
That having been said, I know of two helicopter pilots who taught themselves how to fly a helicopter - without any instruction - in real helicopters....
(if that doesn't get the thread going, I don't know what will)