They should. Just because you're in reader view just displays the page slightly differently to make reading it easier, but it still loads the same in the background.

Thanks for the response! I realized I could also test this out by going to the Scroll website where it shows the articles you've read and how far down you scrolled. It looks like when one is using reader view, Scroll registers that the article is being read, but does not detect how far down you scroll on the page (which I believe they use to determine the allocation of the subscription fees between websites).