Unless they state otherwise, I just assume that it's a half square triangle and the size refers to the finished size of the square. You can usually look at the picture of the quilt to verify that it's a hst.
I've wondered this too. So if they end up with a 5" hst, they started out with two 5.5 squares? right?
In my day as an elementary teacher and equilateral triangle is the same measurement on all sides.