The point of Starship is to launch hundreds at once, several times a week if it goes as planned (that's a few years away.) Forget Mars colonization, the only practical use for such a booster is to fight a war in LEO.

There's currently more than 3,000 satellites in the constellation. Killing scores or even hundreds isn't enough. The only known EMP weapons that could really impact the constellation is nuclear, and at that point, knocking out Starlink is the least of our worries.