Well, no; there's two problems now. The first one is that your browser will handle click events on invisible and near-invisible layers. The second one is that your browser will allow click events to flow through opaque and near-opaque layers.
A lot of web Javascript would be useless if events didn't bubble, and being able to define invisible click areas is useful in a variety of contexts.
Sucks that a few people are going to be malicious about it but I think the benefits outweigh the drawbacks.
Invisible click areas as you called it are not the same as multi-layered click targets imho.
I hope this doesn't mean the end of niche browsers, or at least not those built on well-known rendering engines like WebKit.