I love popups. Used properly, they are a great way to parse out information that your users might need together, but separately. Like a popup that delivers a handout or instructions to an in-course activity. I also tend to use popups for a majority of my in-course videos.
Whether they are “good” or not is subjective. As @mnotermans5114 said, you can move them around and keep them open. This is particularly useful for content where your users should be referring to a handout or other provided content while doing an activity or test.
It’s always best to put popups in their own chapter, so they can be easily found when you are building. I’d also suggest making sure you remove that chapter from the Table of Contents before publishing.