So what happens if an EMP is deployed in the general vicinity (50mi) before the warheads each go their own way? If you get one doesn't that set off a chain reaction if they are still in close proximity to each other. If nothing else their guidance systems would be cooked. Years ago the neutron bomb (EMP) was so small it was considered to be deliverable as a tank shell.
Subs already have that deployment capability, s300's, and more advanced systems, pretty much grounded low level attacks (under 50,000ft)