The reason why pages that have scripts at the top of the page still score an 'A' is because this is not as important as other performance improvements that could be made.
Each rule is weighted, so some rules affect the ySlow grade more than others.
I always put scripts at the bottom. There are very few reasons for needing scripts at the top of your page. The only reason I can think of is you need your JavaScript to execute immediately before anything else in the page, which is quite rare.
