Does the dialog ask whether you will give the site permission to store data on your computer? You can change how the Flash player deal with local storage to a silent option such as allowing sites to store data without asking, or prohibiting them from storing data. This page has the tool to do that as well as a description of how it works:

http://www.macromedia.com/support/documentation/en/flashplayer/help/settings_manager03.html

If the pop-up is something else, like an ad, could you describe it in more detail and maybe link to a video that has this issue?

I doubt that you want to block s.ytimg.com. It serves images and videos to YouTube. You might try Adblock Plus if certain ads are bothering you. An Easylist subscription with it works well.