Universities normally have "site licenses", and they are substantially cheaper than regular academic licenses (the one you buy in the bookstore)...
I think the price is around $20/usable copy for most programs, for example. An unlimited site license most probably costs several k$, but I don't have a number.
The reason is that MS has a strong interest that college students get a lot of exposure to MS programs.
The unversity where I am at, for instance, has an unlimited Windows 98, Office 2000 and similar licenses. They do, however, only have a smaller number of Adobe product licenses, and therefore there is a specific program running with them to make sure they don't exceed the number.
So, yes, there are two cases, one with unlimited licensing, one with limited numbers.
In the bookstore, you get a single license, and it has nothing to do with a site license, it's just a regular academic version, with the licensing agreement between you and the vendor and not the university and the vendor.
Edit: Some clarifications.