The last time you used Google and it auto-suggested a result, you saw those terms/keywords. That impression may not have been tracked, but think of how useful that could be for branding. You type in "ACME" and you see "Acme Rubberbands."
Now you've associated the product with the brand whereas you may not have before, and you may well have been prompted to navigate to that search query.

It's also relevant to reputation management. If you've got a negative suggested query, you'd want to suppress that.

Googlebot is most definitely able to run scripts: http://www.seomoz.org/blog/just-how-smart-are-search-robots How is your link positioned inside the script? Is there visible anchor text anywhere in the widget/pop-up window?