Pop-ups that cause an annoyance is almost always because of proprietary JavaScript (as free JavaScript that respects the user is unlikely to spam them with annoying popups).
I tend to avoid running JavaScript, free or nonfree, as really, 100% of websites work better without JavaScript.
There's plenty of terrible websites that are entirely built on top of javascrap when their only purpose is to display plain text and pictures (articles), disabling javascrap on those will result in getting a blank page, which is good i guess cause you shouldn't be visiting such horrendous sites in the first place (Fandom being one example of this if not the worst).