Savvy marketers aren't measuring clicks, they're measuring conversions and they tie their marketing spend to sales leads and to revenue generated. Ads that generate clicks but no sales don't last long.
And sure it's harder to measure a branding campaign in any medium (though people certainly still do it). You don't necessarily care about clicks at all in that scenario. Brands have been figuring out ways to measure the effectiveness of campaigns on offline sales since long before the internet.
Click fraud is an issue for the industry, but it's a small one. It's simply not true that "most clicks" are fraud. And, in any event, digital ad spend continues to grow. So if Buzzfeed and Vice are in a slump it's not because advertisers are shying away from digital.
There is absolutely garbage inventory mixed in, and lots of solutions to try to minimize the impact of that, but to assume that these major brands don't know how this all works is naive.
Further, just as an example, both Google and FB have very solid options for importing offline conversions which are relatively easy to map back to an audience ID of some sort.