I am a blond American woman in her twenties. I am planning a trip to Turkey this fall, and will be traveling with another young female.
I have been told that women traveling alone are sometimes mistaken for hookers by Turkish men. Has anyone had any experience with this? Does anyone have any advice on how to prevent it?

"how to prevent it?"
Leave all your glittering outfits at home.
When you check into a hotel make sure that you have some luggage with you,you will look suspicious checking into a hotel with carrying only your make-up bag.
other than that you will be fine,we get millions of blonde female tourists every year in Turkey.Try not to worry toomuch.

Unfortunately it's a "Man Thing" and Turkey is just a little bit worse for it than some other countries and nowhere near as bad as others.
#2
Turkey is not "just a little bit worse ".
There are quite a few countries between southern Europe, South - SE Asia, and Africa, where women aged 20-60 come to get local boyfriends.