This is done sometimes, but has only limited success. Most users will click the "your computer is infected, click here to upgrade!" fake windows presented by webpage JS on a PC. You really think an app-fade effect will help enough to make a difference? It would help a bit, but not much.

> they don't show an app icon in that view? Why not?

Because then malicious/spammy applications would present fake alerts, which were non-badged normal popups, and add false badges. I guess you could badge everything, and push the problem onto apps whose icons look similar enough to other apps when shrunk down to whatever size your badge is. Either way, it still ends up in the same boat: probably a little bit helpful, but not much.