From my understanding, this is part of why reader mode is not standardized or well documented. Its heuristics are definitely revised, likely in part to address this.
Reader mode probably has a pretty low impact on ads. The full page is usually going to load before you activate reader mode, so the only ads it's actually hiding from you are ones below the fold, which are much lower value to begin with.
Yes, but at some point advertisers have to realize that people who use reader mode don't actually see the ads. The ads might load, but the user is just staring at the reader mode button waiting for it to turn on.