I just spoke to my sweetwater rep about this.
They assured me that I would get a free upgrade (academic). I think what the pricing that showed an academic crossgrade was simply how much it would cost to start on the upgrade track.
For example:
Let's say you bought PT9 outright, no academic anything. After purchasing, you become a student. Then, let's say when 10 came out, you crossgraded to 10, but did so as a student, and thus paid the 'student/academic' upgrade price this one time. Now, since you have that student crossgrade that you paid for to jump from 9 to 10, you are now on the student/academic upgrade track and will pay nothing to get future upgrades *unless you have to get a next gen iLok, like me