Well yes, if you drop UIKit, then indeed you'd have to replace it with something, preferably CSS and Javascript, if really needed. I'm not gonna dispute about the brilliance of UIKit, cuz' that's highly subjective.
You say that in your latest project you used ~53 kB of minified Javascript and ~20 kB of CSS from UIKit alone. It's hard to tell if it's a lot or not without knowing what kind of project it is (applications have different needs than webpages), either way, file size is not an issue for you. In case of Automad it IMHO is somewhat an issue. Nevertheless it is was a conscious (I suppose) joice of its creator to use it, so there's not much that can be done about it.
