I am just worried that a high atmospheric EMP will take out the dots
Well, that's a valid concern, but...that's why you keep the iron sights on as back up!
As Hackathorn observed (which you'd know if you'd actually watched), those who train heavily with a red dot on their handguns will not instantly switch to their irons when the dot disappears. Their minds are conditioned to look for the dot and, in an emergency, that's exactly what they will do when it goes off, i.e., bob their heads around looking for it.
