I think it's a little bit of what everyone's said, personally. I think at first she may have put on a little squeakiness in order to please (I still to this day can't listen to her original version of "Depend on you" without cringing), since her Japanese fans are often saying how that sounds cute.
But then, listening to her now, you can still tell her voice is kind of high by nature, but it's not squeaky as much as it used to be.
And even further, listening to her live, I believe that's the closest to her pure voice. The acapella portion of "A Song for XX" in A MUSEUM is good evidence of this.
So yes, I'd say Ayu's singing voice is real, although she's been known to 'spice it up' with some kawaii squeakiness at times. She herself even said she sang higher in "HONEY" to make it sound cute.
