Nuclear bursts in the stratosphere will also shower the place with protons. Those will collide with metal boxes, knocking electrons off the inside surfaces of the box. That secondary emission must be handled using a box inside a box.
EMP is a problem only if you are really close to the burst. For example, a 10KT ground burst causes EMP that can cause little damage when over 2 miles away. Big bombs make a higher density; however, I don't think they travel much farther than affects of the burst itself. High altitude burst with large warheads are more troublesome, but EMP from those things still follows the inverse square law. The military is concerned about all of this because the nukes will be aimed at their stuff. They want their electronics to survive a near miss.
I’m not talking about high tech but changes in configuration of the technology. Miniaturization brings a whole new level of hardness to electronics. EMP effectiveness has changed wrt to the things you are stating/citing. EMP effects can be expanded by number of weapons used, configuration of munition(s) and method of deployment. Precision deployment methods are growing in leaps and bounds.