Why do some channels like Mr. Beast not have that little "Contains paid promotion" popup even though the video is sponsored? Eg. Mr beasts latest video.

Because being sponsored means they were paid by a third party and depending on your location there may be laws that dictate what you have to disclose. From Googles support site:

Sponsorships are  pieces of content that have been financed in whole or in part by a third party. Sponsorships generally promote the brand, message or product of the third party without integrating the brand, message, or product directly into the content.

Note that laws that apply to you may define paid promotions differently. Creators and brands are responsible for understanding and fully following legal obligations to disclose paid promotion in their content according to their jurisdiction. Legal obligations might include when and how to disclose and to whom to disclose.

So in short, if you made money from a third party to produce a video, even if the sponsor doesn't require you mention it, it's in your best interests to disclose that information. Mr. Beast and others like him are clicking the little box that says “My video contains paid promotion like a product placement, sponsorship, or endorsement.” so they don't end up on the wrong side of things.

/r/NewTubers Thread