Hi,
If you remove it, you won't get the cart module to update dynamically when the AJAX mode is activated. The system rely on that div being there in order to work.
Maybe you don't need that capability on your website but plenty of other users do need it, so we can't remove it.
As you say, hard coding HTML or CSS is not a good practice, and that's why we try to avoid it, even though there are still a few places where that it the case (you mentioned the filters and that's something we'll change in the future).
Regarding the cart module, with next version of HikaShop the cart module will have a layout for its HTML display so you'll be able to override it in your template and remove that HTML if you want, like any other view of HikaShop.
And there is no need to be harsh in your messages. We understand you the same.