In a webmaster hangout, Google’s John Mueller said that Google might give higher priority to the contents of an advertising popup instead of the content behind the popup:
If you can tell that someone is already browsing your website, and they’re looking at stuff, or maybe they are reading through a longer page, then maybe it makes sense to let them know, “Hey, if you really like this, is a great way to kind of keep in touch, stay up to date with the new changes.” And maybe that makes sense to kind of, like you said, delay it into the session.
But let’s say that doesn’t happen. Is there a risk that Googlebot might give higher priority to the content on the pop-up instead of the content behind it? […] That can definitely happen.
You can view the video here: